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Molecular conductanceValkenier-van Dijk, Elisabeth Hendrica

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Molecular ConductanceSynthesis, Self-Assembly, and Electrical Characterization

of π-Conjugated Wires and Switches

Hennie Valkenier

The work described in this thesis was performed in the research group Chemistry

of (Bio)Molecular Materials and Devices, Molecular Electronics, Stratingh

Institute for Chemistry and Zernike Institute for Advanced Materials, University of

Groningen, The Netherlands. This research is financially supported by NanoNed,

funded by the Dutch Ministry of Economic Affairs (project GMM.6973).

Cover design: Bart, Roelie, and Hennie Valkenier

Produced by: F&N Boekservice

Zernike Institute PhD thesis series 2011-12

ISSN 1570-1530

ISBN 978-90-367-4943-5 (printed version)

ISBN 978-90-367-4942-8 (electronic version)

Copyright 2011, E. H. Valkenier-van Dijk

RIJKSUNIVERSITEIT GRONINGEN

Molecular ConductanceSynthesis, Self-Assembly, and Electrical Characterization

of π-Conjugated Wires and Switches

Proefschrift

ter verkrijging van het doctoraat in de Wiskunde en Natuurwetenschappenaan de Rijksuniversiteit Groningen

op gezag van de Rector Magnificus, dr. E. Sterken,in het openbaar te verdedigen op

vrijdag 1 juli 2011om 16.15 uur

door

Elisabeth Hendrica Valkenier - van Dijk

geboren op 11 augustus 1983te Roden

Promotor: Prof. dr. J. C. Hummelen

Beoordelingscommissie: Prof. dr. M. Mayor

Prof. dr. Th. Wandlowski

Prof. dr. ir. H. S. J. van der Zant

Table of ContentsChapter 1 Molecular Electronics 7

1.1 Introduction ...................................................................................................... 81.2 π-Conjugated Molecules in Organic Electronics ................................................81.3 Opportunities of π-Conjugation Topologies ....................................................111.4 Methods for Conductance Measurements .....................................................151.5 Our Matrix Approach ......................................................................................221.6 References and Notes .....................................................................................26

Chapter 2 Anthraquinone- and Anthracene-based Molecular Wires and Switches 31

2.1 Introduction .................................................................................................... 322.2 Synthesis of the Anthraquinone- and Anthracene-based Molecular Wires .....372.3 Optical Properties ...........................................................................................432.4 Redox-Switching of the Anthraquinone Wire ..................................................462.5 Energy Levels .................................................................................................. 502.6 Crystal Structure ............................................................................................. 522.7 Conclusions .................................................................................................... 532.8 Experimental Section ......................................................................................542.9 References and Notes .....................................................................................66

Chapter 3 Controlling the Formation of Self-Assembled Monolayers of Conjugated Thiols on Gold 69

3.1 Introduction .................................................................................................... 703.2 Synthesis of Oligo(phenylene ethynylene)s .....................................................723.3 Deprotection of Acetyl Protected Thiols and the Formation of SAMs on Gold 743.4 Composition of the SAMs by XPS ....................................................................873.5 Electrochemical Characterization of the SAMs ................................................903.6 Large Area Molecular Junction Devices ...........................................................933.7 Conclusions .................................................................................................... 953.8 Experimental Section ......................................................................................963.9 References and Notes ...................................................................................104

Chapter 4 Trends in the Conductances of Three Series of π-Conjugated Molecular Wires 109

4.1 Introduction .................................................................................................. 1104.2 Synthesis of the Molecular Wires .................................................................1134.3 Optical Properties and Energy Levels ............................................................1154.4 Conductance Measurements ........................................................................1164.5 Discussion .................................................................................................... 1194.6 Transport Calculations ..................................................................................122

5

4.7 A Molecule in a Breaking Junction ................................................................1244.8 Conclusions ..................................................................................................1274.9 Experimental Section ....................................................................................1284.10 References and Notes .................................................................................133

Chapter 5 The Influence of the π-Conjugation Pattern on Conductance 137

5.1 Introduction .................................................................................................. 1385.2 Formation of Self-Assembled Monolayers ....................................................1415.3 Conductance Measurements using Conductive Probe Atomic Force Microscopy .............................................................................1475.4 DFT-NEGF Transport Calculations .................................................................1485.5 Conductance Measurements in EGaIn Junctions ..........................................1505.6 Conductance Measurements in Large Area Molecular Junctions ..................1525.7 Single Molecule Conductance Measurements ..............................................1535.8 Conclusions ..................................................................................................1555.9 Experimental Section ....................................................................................1575.10 References and Notes .................................................................................160

Chapter 6 Methano[10]annulene in Molecular Wires and Polymers 1636.1 Introduction .................................................................................................. 1646.2 Synthesis of 2,7-Dibromo-1,6-methano[10]annulene ...................................1666.3 Methano[10]annulene-Based Molecular Wire ..............................................1686.4 Copolymer of Methano[10]annulene and Bithiophene ................................1716.5 Conclusions ..................................................................................................1766.6 Experimental Section ....................................................................................1776.7 References and Notes ...................................................................................186

Chapter 7 The Matrix Approach Revisited 1897.1 Results from the Matrix Approach ................................................................1907.2 A Comparison of the Conductance of Monothiolated and Dithiolated OPE3 1987.3 Perspectives of Molecular Electronics and π-Logic .......................................2037.4 References and Notes ...................................................................................206

Publications ...............................................................................................209

Summary .................................................................................................211

Samenvatting .............................................................................................215

Dankwoord ................................................................................................223

6

Molecular Electronics

Chapter 1Molecular Electronics

This chapter introduces our Matrix Approach to study the molecular conductance of π-conjugated wires and switches. We explain the opportunities of conjugation topologies for molecular electronics and describe various methods by which molecular conductance can be studied.

7

Chapter 1

1.1 IntroductionLife has changed significantly in the last centuries. Thanks to inventions of for

instance engines and electric lightning during the 19th century, products are no

longer made by hand but mechanically crafted in large factories, transportation

became easier, as did life at home. After the industrial revolution, the 20th century

saw an electronic revolution to such a point that life without computers or internet

is unimaginable. Current developments are the miniaturization of electronics and

the replacement of classical semiconductors as silicon, germanium, and gallium

arsenide by organic materials in so-called "organic electronics". In this thesis we

will combine both these developments and we will investigate the potential use of

single organic molecules (or a single layer of molecules) in electronics,1 aptly called

"Molecular Electronics".2 The ultimate aim would be to construct electronic

circuits of molecules only.3 In Section 1.3 we present how molecules could be

wired and how logic operations could be performed with these molecules, in

theory. However, in experiments we cannot go that far yet. Even the conductance

measurements on single molecules are not trivial and subject of debate. Therefore,

we investigate the electrical conductance properties of molecules by integrating

these molecules in metal-molecule-metal junctions, as we describe in Section 1.4.

By studying series of molecules in different metal-molecule-metal junctions, as

shown in Section 1.5 we aim at finding the influence of molecular structure on the

electrical conductance. We will first introduce the type of molecules this thesis

deals with: π-conjugated molecules.

1.2 π-Conjugated Molecules in Organic ElectronicsThe molecules and polymers shown in Figure 1.1 are important in organic

electronics and are used in commercially available organic solar cells or other

organic devices. These structures have in common that they are made-up almost

entirely of π-conjugated carbon frames, which can be recognized in these drawings

by their double and single bonds. It is this π-conjugation which gives the molecules

their semi-conducting properties.

8


The description of π-conjugation as a pattern of alternating single and double

bonds is based on valence-bond theory. An alternative way of considering bonding

in molecules is molecular orbital theory, which states that the atomic orbitals of

the atoms in a molecule are combined to form the same number of molecular

orbitals. Energy is gained with this combination when the symmetry of the orbitals

allows overlap and a bond is formed. The molecular orbitals that are the lowest in

energy are in general related to the σ-bonds (which hold the atoms together).

Carbon atoms have four electrons in the four valence atomic orbitals: 2s, 2px, 2py,

and 2pz. These atomic orbitals hybridize when involved in the formation of a -σbond. The carbon atoms in the π-conjugated cores of the molecules in Figure 1.1

are sp2 hybridized: the 2s, 2px, and 2py mix to form three sp2-orbitals, which are

involved in -bonds. The σ pz-orbitals, that are oriented perpendicular to the -σbonds, remain and can combine to form molecular orbitals, as shown for ethene in

Figure 1.2a. The "bonding molecular orbital" corresponds to a π-bond (the second

line of each double bond in Figure 1.1). The gain in energy from the formation of

a π-bond is much smaller than for a -bond. σ

The (opto)electronic properties of molecules are dominated by their frontier

orbitals: the highest occupied molecular orbital (HOMO) and the lowest

unoccupied molecular orbital (LUMO). Since the bonding orbitals that are

composed from pz-orbitals are in general higher in energy than those involved in σ-

bonds and the corresponding (unoccupied) anti-bonding molecular orbitals are

relatively low in energy (compared to anti-bonding σ-orbitals), the HOMO and the

LUMO of conjugated molecules are constructed from linear combinations of the

pz-orbitals.

9

Figure 1.1 Examples of conjugated molecules and polymers that are applied in organic electronics: a. pentacene, b. regioregular poly(3-hexylthiophene) (P3HT), c. a poly(phenylene vinylene) (MDMO-PPV), and d. [6,6]-phenyl-C61-butyric acid methyl ester (PCBM).

Chapter 1

The more pz-orbitals are present in the conjugated system, the more molecular

orbitals are formed and the closer the spacing in energy between these orbitals, as

is illustrated with 1,3,5-hexatriene in Figure 1.2b. Therefore, larger conjugated

systems, in general, have a smaller HOMO-LUMO gap. This facilitates the

introduction of charges (either positive or negative, due to oxidation or reduction

of the molecule), which makes conjugated organic materials suitable for

applications in electronics.

In 1977 Shirakawa, MacDiarmid, and Heeger found the conductivity of films of

trans-polyacetylene to increase over seven orders of magnitude upon treatment

with iodine vapor,4 for which they were awarded with the Nobel prize in 2000.

Iodine oxidizes polyacetylene and thus introduces positive charges ( i.e., doping),

which are stabilized with I3- counter ions. Alternatively, charges can be introduced

by an electric field, for instance when these polymers are used as the

semiconductor in field-effect transistors (FET), or by light in organic photovoltaics

(solar cells). Due to resonance structures (valence bond theory) or delocalized

orbitals (molecular orbital theory) the charges are mobile within the π-conjugated

10

Figure 1.2 a. pz-Orbitals of ethene and their combination into molecular orbitals, with the corresponding energy diagram. b. pz-Orbitals of 1,3,5-hexatriene.

Figure 1.3 Charges that are introduced in a π-conjugated polymer chain are mobile, as represented by resonance structures.


polymer chains (Figure 1.3). Furthermore, they can 'hop' from one chain to the

other (or from one part of a chain to another part of this chain), which makes

conjugated polymers conductive materials.

1.3 Opportunities of π-Conjugation Topologies

1.3.1 Cross-conjugation

In the previous section we have discussed the properties of molecules with a

framework of sp2 hybridized carbon atoms. The strict pattern of alternating single

and double bonds is called "linear conjugation" or "through conjugation". An

alternative conjugation pattern is cross-conjugation, which is defined as “three

unsaturated groups, two of which although conjugated to a third unsaturated

center are not conjugated to each other”.5 In Figure 1.4a the pathway between A

and C is linear conjugated, just as the pathway between B and C, whereas the

pathway between A and B is cross-conjugated. Because all sp2 hybridized carbon

atoms in this structure have a perpendicular pz-orbital and there is overlap between

these pz-orbitals, cross-conjugated molecules do show delocalization of electron

density, although less than linear conjugated molecules.

Cross-conjugation originating from methylene side groups (Figure 1.4a and b) or

substituted alkenes (Figure 1.4c) was reviewed by Tykwinsky.6 We should note that

also meta-substituted phenylenes (Figure 1.4d) are cross-conjugated. Cross-

conjugated building-blocks as the thienothiophene in Figure 1.4e have been

integrated in polymers and used in field-effect transistors, resulting in an improved

air-stability and good mobility.7 Very recently, cross-conjugated molecules have

started to draw a lot of attention in the molecular electronics community due to

11

Figure 1.4 Examples of cross-conjugated molecules and building blocks.

Chapter 1

calculated quantum interference effects. This quantum interference effect lowers

the molecular conductance at low bias voltages significantly,8 as we will discuss in

Chapter 5.

1.3.2 Omniconjugation

To realize electronic circuits of molecules only, π-conjugated molecules are the best

candidates due to their conducting properties (Section 1.2). However, charge

transport through these circuits should be through these molecular wires (for

instance in the way that the carbocation "moves" through the chain in Figure 1.3)

and not by hopping. Therefore we need linear conjugated pathways. A common

method to design circuits of conjugated molecules is by interconnecting different

parts via substituted benzene rings.910

-11 However, as we mentioned in the previous

sections, the used meta-substitution of phenyl rings results in cross-conjugated

pathways between the different parts of these molecules. Marleen van der Veen, a

member of our group, has designed a more feasible alternative, so-called

omniconjugated structures: “Omniconjugation is defined as the property of

molecules, having direct linear π-conjugated pathways between all connected

moieties.”12 Examples of omniconjugated structures are given in Figure 1.5.

12

Figure 1.5 Examples of omniconjugated structures with two terminals (a), three terminals (b) and four terminals (c-f).


1.3.3 π-LogicOmniconjugated molecules do not only have potential as interconnects in all-

molecular electronic circuits, they can also be used to design molecules to perform

logic operations. This concept was developed by Marleen van der Veen13 and will

be briefly explained in this section. Small circuits are used in current electronic

devices to perform logic operations and it would be useful to replace these circuits

by single elements. De Silva and co-workers came up with the idea to use

molecules as logic elements.14 They designed a molecular AND gate, in which

ionic inputs determine the fluorescence output. Other molecular logic gates

followed,15 most of which yield optical signals as output. However, electrical

outputs are desired for integration in solid-state devices. Rather complex examples

are the OR and AND gates based on the molecular rectifier of Aviram and

Ratner.1,16

Simple logic gates can be constructed from combinations of switches. The

molecule in Figure 1.6a is an example of a switch: the pathway between T1 and T2

is linear conjugated (bold, defined as "on" or "1") when input channel A is

connected via single bonds. Upon oxidation of the molecule (or passage of a

soliton from A1 to A2, which converts all single bonds into double bonds and vice

versa), A1 and A2 become connected via double bounds and the pathway from

terminal T1 to T2 becomes cross-conjugated ("off" or "0"). Two of these switches

13

Figure 1.6 a. An example of a switch. Two of these switches can be combined in series (b) or parallel (c) to form logic NOR and NAND gates, of which the corresponding truth tables are shown.

Chapter 1

can be combined, which gives two input channels (A and B), each of which can be

either connected by exocyclic single bonds (0) or by exocyclic double bonds (1).

This gives four possibilities. Depending on the connection of the two switches,

either in series (Figure 1.6b) or in parallel (Figure 1.6c), a logic NOR gate or a

logic NAND gate is obtained.

This method of connecting switches only allows the design of a limited set of logic

gates. Multiple NAND gates can in principle be connected in such a way that more

complex logic gates like XOR and XNOR gates are obtained. Unfortunately, this

leads again to rather large and unrealistic designs. A more elegant approach is the

use of omniconjugated molecules to construct Boolean logic gates. The pyracylene

compounds as drawn in Figure 1.5d and e are good candidates to be functionalized

with additional terminals. Proper positioning of the two input channels (A1-A2 and

B1-B2) and the read-out channel (T1-T2) allows the construction of 15 out of 16

Boolean logic gates.13 Examples of a NAND-gate (more compact than the one in

Figure 1.6c) and a XOR-gate, which is in general hard to design, are given in

Figure 1.7.

This concept of using relatively compact conjugated molecules with six terminals

to perform logic operation is called "π-logic".13 One of the main assumptions of

this concept is that the conductance through linear conjugated pathways and cross-

conjugated pathways is different. Linear conjugated pathways are expected to have

a higher conductance ("1") than cross-conjugated pathways ("0"). The main

14

Figure 1.7 The four different states of a NAND gate (a.) and a XOR gate (b.), based on pyracylene molecules.


objective of this thesis is to find convincing evidence for this assumption by means

of conductance measurements. This would establish this switching principle as the

fundament for fast and efficient molecular logic operations.

1.4 Methods for Conductance MeasurementsBefore we can use molecules as components of electronic circuits,17

18

-1920

21 we have to

learn how single molecules or a single layer of molecules (i.e., a self-assembled

monolayer, SAM) behave electrically. In other words: we need to measure the

current through the molecules upon applying a voltage. For that, we have to

connect the molecule to (at least) two electrodes. Many methods have been

developed to contact molecules, as reviewed by several groups.222324

-2526

27 We will

describe a few techniques for conductance measurements of conjugated (di)thiols

in the following section, not aiming at giving an elaborate overview of all possible

techniques. Instead, we will mainly focus on the techniques we have been involved

with via collaborations and to which we will return later in this thesis. Theoretical

descriptions of charge transport through molecular junctions can be found in

several reviews.2829

-30

31

1.4.1 Mechanically Controllable Break Junctions

A mechanically controllable break junction (MCBJ) consists of two sharp

electrodes whose spacing can be adjusted and over which a voltage can be applied

(Figure 1.8). The first MCBJ was prepared from a very thin metal wire that was

glued to a flexible substrate.32 A piezo element and two counter supports enabled

controllable bending of the substrate. The wire was deeply notched and bending of

the substrate caused a fracture in the wire. In 1997 Reed et al. reported on the

conductance of benzenedithiol, using a similar setup.33 They placed a glass tube on

the junction and filled this with a mM solution of 1,4-benzenedithiol in THF, to

form a SAM of these molecules on the gold wire. They broke the wire by bending

the substrate and brought the electrodes together until a spacing of about 8 Å (the

calculated length of the dithiol). In this position a voltage was applied and current-

voltage (I-V) measurements were performed, from which was concluded that a

single molecule or a few molecules were measured.

15

Chapter 1

Van Ruitenbeek et al. succeeded in downscaling the device dimensions by two

orders of magnitude.34 They prepared break junctions using electron beam

lithography on a bendable phosphor-bronze substrate, which resulted in devices

with a free hanging metal bridge of about 2 m (μ Figure 1.8b). When such a

lithographically defined junction is broken, two atomically sharp nanometer-wide

electrodes are formed. MCBJs can be operated either in a liquid environment35 or

in UHV and at low temperatures (4.2 K).36 This results in highly stable junctions37

with control over the spacing between the electrodes. Several conjugated molecules

have been studied in MCBJs by recording I-V curves.3839

-40

41 However, since the shape

of the gold electrode and the binding of the molecules vary from junction to

junction, statistical approaches have been introduced to increase the reproducibility

of the measurements.4243

-44

16

Figure 1.8 a. Schematic of a lithographically defined mechanically controllable break junction in which the displacement of the pushing rod (w) defines the spacing between the electrodes (d). b. Scanning electron microscopy image of the suspended gold bridge of three lithographically defined break junctions in parallel. c. Schematic of a conjugated molecule in a break junction.

Figure 1.9 a. Schematic of the STM tip trajectory when imaging a mixed SAM at constant current mode. b. STM image of a mixed SAM of OPE3 and dodecanethiol on gold (180x180 nm, height scale is 25 Å). This image shows the terraces of the gold surface, two differently packed phases of dodecanethiol molecules (small difference in contrast) and bundles of OPE3 molecules as white spots.


1.4.2 Scanning Tunneling Microscopy

The first Scanning Tunneling Microscope (STM) was built by Binnig and Ruhrer

from IBM Zürich in 1981, for which they were awarded with the Nobel Prize in

Physics in 1986. A metal tip is brought in close proximity to a conducting surface

and a bias voltage is applied between the tip and the surface. A STM can be

operated at constant current mode, in which the height of the tip is adjusted by a

feedback loop in such a way that the current remains constant when a surface is

scanned (line by line), which results in an image of the surface.45 Molecular

resolution is easily achieved nowadays.

The conductance of conjugated molecules has been studied by STM via different

approaches. An approach that was first reported in 1996 is STM imaging of mixed

SAMs.46 First a SAM of alkanethiol molecules is grown on a gold surface.

Conjugated thiols (or dithiols) are subsequently inserted by immersion of the

alkanethiol SAM in a solution with a low concentration of these conjugated

molecules. Since the conductance of these molecules is higher than that of the

surrounding alkanethiol molecules, the tip has to move up (and increase the gap

between tip and SAM) to retain the tunneling current constant (Figure 1.9a). The

conjugated molecules appear in the STM image as light spots (Figure 1.9b). The

"apparent height"47 of these spots is a measure for the conductance of the

conjugated molecules.484950

-51

52 Disadvantages of these method are that the formation

of mixed SAMs is not trivial and that conjugated thiols tend to insert at defects53 or

as bundles of molecules (as is the case in Figure 1.9). Furthermore, the apparent

height could depend on the packing of the surrounding alkanethiol molecules, on

the binding of the conjugated thiol to the gold surface, on the imaging parameters,

and on the shape and cleanliness of the tip, which obfuscates the comparison of

images. Changes in the binding of the conjugated thiol to the gold surface have

been observed as "stochastic switching".5455

-56 An approach to overcome these

problems is to study in situ switching of the molecules by external stimuli as light57

or electrochemical potential.58

Recording I-V curves at specific spots above a SAM (often combined with imaging)

is an alternative approach on molecular conductance.59 A disadvantage is the

presence of an unknown air (or vacuum) gap between the molecule and the tip.

A third approach to study the conductance of single molecules with an STM setup

is the STM break junction approach as introduced by Tao in 2003.60 An STM tip is

17

Chapter 1

brought close to the SAM, after which the feedback of the STM is turned off. The

STM tip is then pushed into the substrate and subsequently retracted, while the

current is recorded (Figure 2.1). This results in the formation of molecular

junctions, similar to those by the MCBJ technique as described in the previous

section. An advantage is the speed of a STM setup, which allows the collection of

thousands of curves (required for a histogram) in a few hours. Instead of pushing

the STM tip into the surface, a soft contact approach can be used, in which the tip

only gently touches the SAM and not the underlying metal surface61 or the tip can

be placed at different distances from the surface and the current can be recorded,

while waiting for a junction to form.62 The STM break junction approach is

generally applied in a liquid environment and can be combined with in situ

electrochemistry.63 More details on STM break junction measurements are given in

Chapter 4.

1.4.3 Conductive Probe Atomic Force Microscopy

Another scanning probe method that is frequently used to study molecular

conductance is conductive probe atomic force microscopy (CP-AFM). Where in

STM imaging a gap between the tip and the monolayer is present, CP-AFM is used

in contact mode. The use of a conductive tip (for instance coated with gold) allows

to measure the current between the tip and the sample on a specific spot on the

surface. Single conjugated molecules (or bundles of these molecules) can be

studied when first a mixed SAM is formed with conjugated dithiols inserted in a

SAM of alkanemonothiols.6465

-66 Subsequently this mixed SAM is immersed in a

18

Figure 1.10 Schematic of the STM break junction approach, in which the STM tip is brought into contact with the gold substrate and then withdrawn.


solution of gold nanoparticles, which bind on the free thiol groups of the inserted

conjugated molecules (Figure 1.11a). These gold nanoparticles can be observed in

an AFM image and then be contacted with the CP-AFM tip, which makes it

possible to measure I-V curves on the single (bundle of) molecule(s). Mixed SAMs

coated with gold nanoparticles have also been investigated by STM.67

A more straightforward approach is to directly contact a densely-packed SAM of

conjugated molecules with a gold-coated AFM tip and measure the I-V

characteristics of the SAM (Figure 1.11b).68 This method is developed and

described in detail by Frisbie's group.69 We estimate that the number of molecules

that are contacted this way is in the order of hundreds.

1.4.4 Liquid Metal Junctions

One of the challenges of contacting a SAM over a larger area to measure its

conductance is to make a decent contact without damaging the SAM. Liquid

metals are good candidates to form the such a top contact. Mercury has been used

in several groups for this purpose.7071

-72

73 A disadvantage of mercury is that it only

forms stable contacts when surrounded by an alkanethiol SAM and in a liquid

environment. When a SAM of conjugated thiols is the object of study, a tunneling

current is measured from the metal substrate through the conjugated thiol and the

alkanethiol to the mercury, thus through two monolayers.

19

Figure 1.11 a. Schematic of a gold coated AFM that contacts a gold nanoparticle on a conjugated molecule, which is inserted in an alkanethiol SAM. b. Schematic of a gold coated AFM tip which directly contacts a SAM of conjugated molecules.

Chapter 1

An alternative liquid metal is the eutectic alloy of gallium (75%) and indium

(25%), abbreviated as EGaIn, with a melting point of 15.5°C.74 Though EGaIn is a

liquid, the thin shell of gallium oxide (~1 nm) makes that it does not necessarily

has a drop shape, instead conical tips can be formed (Figure 1.12). This allows its

use to contact SAMs in ambient conditions and to measure the I-V characteristics

of the SAM.75,76 The contact area of such a tip is in the order of 10-100 m and isμ

measured for each junction with a high magnification camera.

1.4.5 Large Area Molecular Junctions

The aforementioned techniques all have control over the distance of at least one of

the two electrodes, which allows the formation and breaking of the junction. The

fabrication of Large Area Molecular Junction (LAMJ) devices77 is irreversible,

20

Figure 1.12 a. Photo of a sample in the EGaIn setup, showing the syringe needle with the EGaIn tip in the middle of the photo. b. Microscope image of the formation of the EGaIn tip by withdrawal of the syringe from a sacrificial drop of EGaIn. c. Microscope image of an EGaIn tip contacting a surface (including the reflection of the tip by the surface).

Figure 1.13 a. Schematic of the fabrication procedure of LAMJs, starting with the evaporation of the bottom contact on a silicon wafer, followed by lithographical definition of pores in a photoresist layer. After cleaning the gold, SAMs are grown inside these pores. Then PEDOT:PSS is spin coated on the wafer and the gold top contact is evaporated, after which the excess of PEDOT:PSS that is not covered by the gold top contact is removed (adopted from ref. 77). b. Schematic of the junction.


since the SAM is sandwiched between two solid electrodes. Earlier attempts to

form this type of solid junctions by evaporation of a metal top contact on a SAM

(that was grown on a bottom contact) resulted in shorts due to penetration of the

metal through the SAM,78,79 which limited the junction size80 and the yield of non-

shorted devices.81 These problems were overcome by spin coating a layer of

metallic conducting polymer on top of the SAM before evaporation of the a top

contact (see Figure 1.13).77,82 The water-based suspension of heavily oxidized

poly(3,4-ethylene-dioxythiophene) stabilized with poly(4-styrenesulfonate)

counterions (PEDOT:PSS) is mainly used for this purpose. This trick allows the

formation of stable junctions83 up to 100 m in diameter in over 95% yield.μ 77

Further development of the fabrication process resulted in wafers with over 20000

junctions and in series connection of up to 200 junctions.84

1.4.6 Arrays of Gold Nanoparticles

As alternative to repetitive formation and breaking of single molecular junctions to

obtain statistical data on molecular conductance, arrays of gold nanoparticles were

developed to measure many junctions (both in series and parallel) simultaneously

and obtain average conductances (or resistances) for gold-molecule-gold junctions

that way.85 First gold nanoparticles are synthesized, covered with octanethiol

molecules, and dissolved in chloroform. A drop of this solution is placed at an air-

water interface, where the gold nanoparticles self-assemble into a 2D array (Figure

1.14). This array is transferred onto a substrate using a patterned PDMS stamp and

gold contacts are evaporated. The sheet resistance of the array between these

contacts is measured.

The array can be immersed in a solution of dithiols (for example conjugated

OPE3), that exchange with some of the octanethiol molecules. Since these OPE3

dithiols can bind to two adjacent nanoparticles (and are conjugated), the resistance

of the networks drops with a factor 100-1000 to about the resistance of a single

OPE3 molecular junction. Exchange with OPE3 monothiol molecules lowers the

resistance of the network, though less than OPE3 dithiol molecules.86 The

exchange process has been confirmed by the reversible shift of the UV-Vis

absorption from the surface plasmon resonance of the gold nanoparticles, and

reversible changes in the IR spectra of the networks.87 Different conjugated dithiols

can be inserted in the array via exchange processes and the resulting resistances

can be compared. Alternatively, the inserted molecules can be switched by external

21

Chapter 1

stimuli (i.e., light or redox chemistry) and this switching process can be monitored

by measuring changes in the resistance.88,89

1.5 Our Matrix ApproachIn Section 1.3 we have discussed the concept of using π-conjugated molecules as

logic gates.13 To study this π-logic proposal experimentally, techniques by which at

least three (preferably four) terminals can be contacted are required. In known

three-terminal junctions the third electrode is a gate, which does not directly

contact the molecule(s) as the other electrodes do.90,91 The π-logic idea is based on

conductance differences between linear conjugated and cross-conjugated pathways

between terminals. The main aim of this thesis is therefore to study this difference

experimentally.

22

Figure 1.14 Schematic of a 2D array of octanethiol-covered gold nanoparticles through which the current is measured. Octanethiol molecules (black) can be reversibly exchanged by dithiolated OPE3 molecules (red), which reduces the resistance of the network by two to three orders of magnitude. The inset shows a scanning electron microscopy image of a 2D array of octanethiol-covered gold nanoparticles transferred onto a silicon wafer.


23

Figure 1.15 The Matrix Approach, in which we study the conductance of five series of molecules (left) by various methods (top). The series of molecules are constructed by varying the central unit.

Chapter 1

We have developed an anthraquinone-based switch derived from the structure in

Figure 1.6a.92 This cross-conjugated anthraquinone-based switch becomes linear

conjugated upon (electro)chemical reduction, in solution. In Chapter 2 we describe

the synthesis and spectroscopic properties of this cross-conjugated state of the

switch and several reference compounds that are linear conjugated or have a

broken conjugation pattern. Since the conductance measurements on a single,

switching molecule inside a junction under electrochemical control were found to

be non-trivial, we have broadened our scope, aiming at measuring reliable

conductance data on conjugated molecules. For that, we developed several series

of conjugated molecules, which allow to study trends in the relation between

molecular structure and conductance. All the molecules have oligo(phenylene

ethynylene) (OPE) based structures, of which we either substitute the core

phenylene with any aryl group (as drawn in the left column of Figure 1.15) or vary

the length (second series in Figure 1.15). Though phenylene enthynylene based

oligomers and polymers93 are not as widely used in organic electronics94 as for

instance the phenylene vinylenes (OPVs and PPVs), OPE-type molecules are

present in molecular electronics from the early days.95,96 Advantages of OPE-type

molecules are their rigidity and linearity, which limits the conformational freedom

and therefore rules out one source of variety in conductance measurements. We

use acetyl-protected thiol anchoring groups for all molecular wires.

We study the conductance of these series of molecular wires by several methods

(Section 1.4), ranging from single molecule measurements (MCBJ and STM-BJ),

to measurements on hundreds of molecules (CP-AFM) and areas up to 8000 mμ 2

(corresponding to ~3x1010 molecules97; EGaIn and LAMJ). This study of five

series by five methods constitutes our "Matrix Approach" (Figure 1.15). The

comparison of data from different measurements allows to distinguish trends

caused by the molecular structure and technique dependent trends. All

conductance measurements were performed in collaborations with:

• Veerabhadrarao Kaliginedi, Wenjing Hong, Pavel Moreno García, and

prof. Thomas Wandlowski, University of Bern (STM-BJ and ambient

MCBJ)

• Constant Guédon and Sense Jan van der Molen, Leiden University (CP-

AFM and arrays of gold nanoparticles)

• Eek Huisman, Auke Kronemeijer, Ilias Katsouras, Paul van Hal, Tom

24


Geuns, and prof. Dago de Leeuw, University of Groningen and Philips

Research Eindhoven (LAMJ)

• Davide Fracasso and Ryan Chiechi, University of Groningen (EGaIn)

• Christian Martin, Roel Smit, Diana Dulić, Mickael Perrin, Ferry Prins, Jos

Seldenthuis, prof. Herre van der Zant, and prof. Jan van Ruitenbeek, Delft

University of Technology and Leiden University (UHV and low

temperature MCBJ)

• Víctor García-Suárez and prof. Colin Lambert, Lancaster University

(calculations)

• Troels Markussen and prof. Kristian Thygesen, Technical University of

Denmark (calculations)

In Chapter 3 we describe how high quality, densely packed self-assembled

monolayers of π-conjugated dithiols can be formed, because this is required for

reliable measurements by LAMJ, EGaIn and CP-AFM. Furthermore, we will

demonstrate the influence of the conditions used for the formation of self-

assembled monolayers of OPEs on the resistance by LAMJ. In Chapter 4 we

describe the trends found in STM-BJ measurements on three of the five series.

Chapter 5 discusses the influence of conjugation patterns on the molecular

conductance, as studied by various methods. In Chapter 6 we focus on the

synthesis of methano[10]annulene-based molecular wires and polymers. We return

to the Matrix Approach in Chapter 7 by summarizing all results, discussing

additional results and comparing techniques, to find the main conclusions of this

thesis.

25

Chapter 1

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29

Chapter 1

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30

Chapter 2Anthraquinone- and Anthracene-based Molecular Wires and Switches

We have synthesized an anthraquinone-based redox switch along with anthracene-based and dihydroanthracene-based analogues. The molecules have thioacetate terminals to anchor them to gold electrodes. During the synthesis of the core, the thiols were protected as tert-butyl thioethers, which were converted into acetyl thioesters in the last step. We show that the UV-Vis absorption spectra mainly depend on the conjugation pattern and that the anthracene compounds fluoresce about three orders of magnitude stronger than the anthraquinone compounds. Most important: the anthraquinone-based redox switch can be switched reversibly by electrochemistry or by chemical reduction and oxidation with TDAE and oxygen respectively, as we have shown by cyclic voltammetry, spectroelectrochemistry and NMR experiments.

31

Chapter 2

2.1 IntroductionIn Chapter 1 we have briefly described the principles of π-logic, a concept based on

conductance differences between cross-conjugated and linear conjugated pathways

between two terminals. This concept can be investigated with a molecule in which

the pathway between the terminals can be switched between cross-conjugated and

linear conjugated. We have chosen reduction and oxidation as the trigger for this

switching, because it fits the best in the electrical concept of π-logic, the

conformational changes of the molecule are minimized and it is compatible with

several methods of conductance measurements. This resulted in the design of our

anthraquinone-based redox switch in 2004 (Figure 2.1).1 The pathway from one

sulfur terminal to the other is cross-conjugated in this anthraquinone containing

wire. Upon reduction, the anthraquinone is reduced to the hydroquinone dianion

and the pathway between the sulfur terminals becomes linear conjugated. This

change in conjugation pattern is expected to cause a change in conductance from

low ("off") to high ("on").

In this chapter we will first introduce examples of molecules in which the π-

conjugation is switched by external inputs. We will then describe the synthesis of

our anthraquinone-based redox switch and reference compounds. The synthetic

methodology as developed in this chapter is applied in the syntheses described in

the next chapters. After discussing the optical properties we will show that our

anthraquinone-based switch can be switched reversibly by electrochemical and

chemical methods. In the last sections we will comment on the energy levels and

report a crystal structure of our switch.

32

Figure 2.1 Schematic of the anthraquinone-based redox switch attached to gold electrodes.

Anthraquinone- and Anthracene-based Molecular Wires and Switches

2.1.1 π-Conjugation Switches in the Literature

A switch is used in an electronic circuit to open or close this circuit. It always

needs a “trigger”, for instance someone pushing a button to close the circuit, which

turns on the light. A conducting state and an isolating (less conducting) state are

therefore required. Furthermore, this switching should be reversible.2 Examples of

reversible switching systems in the molecular world are the diarylethene switches.

UV-light is the trigger to switch from the cross-conjugated (open) to the linear

conjugated (closed) state and visible light is used to switch back to the open state

(Figure 2.2a).3,4 The change of conductance of these diarylethene switches upon

irradiation was studied by several methods.

The first diarylethene switches were anchored to the gold surface via thiophene

spacers and these were found to switch only from the closed to the open state in

mechanically controllable break junctions5 and STM experiments.6 This is probably

due to quenching of the excited state of the open switch by the gold electrode. 5 The

use of a phenylene spacer instead of a thiophene improved the reversibility of the

switch when contacted to gold.78

-9 Separating the conjugated system from the thiol

anchoring group by a meta-substituted phenylene allowed reversible switching of

the molecule inside molecular junctions. The linear conjugated (closed) state had a

higher conductance than the cross-conjugated (open) state and reversible switching

between this high and low conductance was possible (Figure 2.2b).10,11 The

switching amplitude decreased over time, since not all molecules switched from

one state to the other: photostationary states were obtained. Measuring a high

conductance means that a larger fraction of switches is closed in comparison to the

lower conductance. An advantage of this optical switch is that it can be addressed

dry and inside a junction as long as there is optical access. Disadvantages are the

aforementioned incomplete switching, the fundamental difficulty to address one

single switch that is embedded in an array of switches by a photon (although these

33

Figure 2.2 a. Schematic of a dithienylethene optical switch with meta-phenyl thiol linkers attached to gold electrodes. It switches from the open to the closed state upon irradiation with UV light and back with visible light; b. Conductance switching upon irradiation of this molecule in an array of gold nanoparticles (adapted from ref 11).

Chapter 2

switches can also be addressed electrochemically12), the conformational changes of

the system (conductance switching cannot be attributed to changes in conjugation

patterns only), and the requirement to decouple the system from the electrodes (the

best working switch has cross-conjugated spacers, thus the system is not completely

linear conjugated from one thiol to the other).

The energy levels of a molecule can be shifted by electrochemical oxidation and

reduction. This concept -referred to as electrochemical gating- is widely used in

electrochemical STM measurements, for instance with oligothiophene and

bipyridyl containing structures.13,14 Several wires containing a tetrathiafulvalene

(TTF) redox center have been synthesized1516

-17 and studied in conductance

measurements.17,18 Even though electrochemical switching was observed, the

conjugation pattern does not change between cross-conjugated and linear

conjugated in these examples, neither in the redox-active molecular wires

synthesized in the groups of Mayor19 and Bryce.20 The π-conjugation does change

in the structures based on extended tetrathiafulvalene (TTF) as presented in Figure

2.3a and b. In contrast to our anthraquinone-based switch, the molecular wires in

Figure 2.3a are linear conjugated from one sulfur terminal to the other and become

cross-conjugated upon oxidation.21,22 Similar to our anthraquinone-based switch,

the structures in Figure 2.3b are cross-conjugated and turn linear conjugated upon

oxidation of the extended TTF.23 For all these extended TTF wires quasi-reversible

oxidation in solution was found, and to the best of our knowledge, no conductance

studies have been published yet.24

34

Figure 2.3 Examples of reported molecules that switch between cross-conjugation and linear conjugation upon reduction or oxidation.


Tour et al. have reported a benzoquinone containing molecular wire (Figure

2.3c),25,26 but did not investigate conductance switching based on reduction and

oxidation. More recently, oligo phenylene vinylene (OPV) based wires with a

hydroquinone head group were synthesized (Figure 2.3d)27 and the thioacetate

terminated molecules were inserted into an octanethiol SAM on gold.28 The

conductance of the OPV wires was found to decrease upon oxidation to the

benzoquinone state as was shown by electrochemical STM imaging.

2.1.2 Anthraquinone- and Anthracene-based Wires and Switches

We have synthesized the anthraquinone-based redox switch (Figure 2.1) with two,

one, and without thioacetate terminals for anchoring to gold electrodes

(compounds 2.1A, 2.2A, and 2.3, see Figure 2.4). The redox-active anthraquinone

unit is separated from the thioacetate anchoring groups by phenyl-ethynyl spacers,

to have a linear and rigid molecule.

Besides these cross-conjugated anthraquinone containing compounds, we made

35

Figure 2.4 Overview of the anthraquinone- and anthracene-based molecules of which the synthesis and properties will be reported in this chapter.

Chapter 2

linear conjugated analogues with anthracene-based cores (2.4A, 2.5A, and 2.6A)

to have stable compounds of which the conductance could be compared with that

of 2.1A. Furthermore, we have synthesized compound 2.7A, of which the π-conjugation is broken by sp3 hybridized methylene groups. The syntheses and

analyses of these compounds will be described in the next sections.

Other possible approaches to switch between a cross-conjugated and a linear

conjugated pathway that were investigated in our group are a pH-switch and a

Diels-Alder switch. The pH-switch is the acridone analogue of the anthraquinone-

based redox switch: the core of the molecule is a cross-conjugated N-methyl

acridone unit, which becomes linear conjugated upon protonation (Figure 2.5a).

This acridone-switch was successfully synthesized by Dr. Daniel J. T. Myles,29 it

was protonated with one equivalent of triflic acid and isolated.30 Attempts to show

reversible switching by UV-Vis spectroscopy failed however. Furthermore, since

this switch includes a heteroatom (with a lone pair) in its π-conjugated core,

reasonable resonance structures can be drawn in which the acridone state is linear

conjugated (with a positively charged nitrogen atom and a negatively charged

oxygen atom) and the protonated state is cross-conjugated (with a positively

charged oxygen atom and a neutral nitrogen atom). Thus, the question arises if this

system actually switches from cross-conjugated to linear conjugated.

36

Figure 2.5 Schematic of an acridone-based pH-switch (a) and an anthracene-based Diels-Alder switch (b) attached to gold electrodes.


Switching of the conjugation pattern could also be achieved by a Diels-Alder

reaction on an anthracene-core (Figure 2.5b) of a linear conjugated wire: reaction

with a dienophile will give a wire with broken conjugation. Heating should result

in a retro-Diels Alder reaction, thus switching back to the linear conjugated wire.

Treatment of compound 2.6B with N-phenylmaleimide gave the Diels-Alder

adduct, which was stable up to at least 180 ˚C.31 Tuning the properties of the

anthracene-core by varying the substituents at the 9,10-positions and a proper

choice of a dienophile should result in a switching system that is compatible with

conductance measurements.

2.2 Synthesis of the Anthraquinone- and Anthracene-based Molecular WiresThe most convenient synthesis strategy for the arylene ethynylene type compounds

as listed in Figure 2.4 is by Sonogashira cross-couplings: a terminal acetylene is

coupled to an aryl (or vinyl) halide by a palladium catalyst and a copper(I) salt as

co-catalyst.32,33 For all Sonogashira cross-couplings in this thesis we have used

dichlorobis(triphenylphosphine)palladium(II) and copper iodide as the catalytic

system in THF, with a secondary or tertiary amine as co-solvent. The Pd(II)

catalyst is reduced in situ to Pd0(PPh3)2 by the amine or by oxidative coupling of

the terminal acetylenes.34 This Pd(0) complex then oxidatively inserts in the aryl-

bromide or -iodide bond. In the meanwhile, the terminal acetylene is activated by

the copper iodide. Transmetallation of the Pd(II) complex and the copper acetylide

results in a Pd(II) complex with the acetylide and the arene. The C-C bond

between the two parts is then formed by reductive elimination and the Pd(0) can

start another cycle.

In a convergent synthesis approach to wires 2.1-2.7, their cores were synthesized in

parallel to the phenylacetylene-based compounds. Cross-conjugated compounds

2.1-2.3 were made by Sonogashira cross-couplings with 2,6-dibromo-9,10-

anthraquinone, as will be discussed in Section 2.2.1. 2,6-dibromo-9,10-

anthraquinone was reduced to various 2,6-dibromo-anthracenes, from which linear

conjugated compounds 2.4-2.6 were synthesized (Section 2.2.2), or to 2,6-

dibromo-9,10-dihydroanthracene, being the core of compound 2.7 (Section 2.2.3).

37

Chapter 2

2.2.1 Cross-conjugated Molecular Wires

The most direct route towards anthraquinone wire 2.1A is a Sonogashira coupling

between 2,6-dibromo-9,10-anthraquinone (2.14) and 4-ethynyl-1-thioacetylbenzene

(2.10). 2.14 was prepared from commercially available 2,6-diamino-9,10-

anthraquinone by a Sandmeyer reaction in 64% yield.35,36 Acetylene 2.10 was

synthesized in three steps from pipsyl chloride (4-iodobenzenesulfonyl chloride),

which was reduced by zinc and dichlorodimethylsilane to 4-iodothiophenol, and

then protected with acetyl chloride to give compound 2.8 in 81% yield (Scheme

2.1).37 Trimethylsilylacetylene was then cross-coupled to 2.8 by a Sonogashira

reaction to give 2.9 in 77% yield and the thiol as a side product. The acetylene was

deprotected by tetrabutylammonium fluoride (TBAF) at low temperature and

under mild acidic conditions to prevent deacylation and 2.10 was obtained in 97%

yield.38

A first attempt to cross-couple 2.14 with 2.10 under the conditions that were used

by Leventis et al. for Sonogashira cross-couplings on bromo-anthaquinones35

failed, while the cross-coupling with phenylacetylene to give 2.3 was reproduced

with a yield of 56% (Scheme 2.2). In a second attempt we used a tertiary amine

(diisopropylethylamine) instead of a secondary amine (diisopropylamine) to

prevent hydrolysis of the thioester. However, no pure 2.1A was isolated. These

problems are similar to those reported by Mayor et al. regarding the Sonogashira

cross-coupling of 9,10-dibromoanthracene with 2.10 in a yield of only 5%.39 To

overcome this problem, they used a tert-butyl protected thiol in the cross-coupling,

and subsequently converted the tert-butyl protected thiol into an acetyl protected

thiol by boron tribromide and acetyl chloride.40 We have adopted this approach

and started with the alkylation of 4-bromothiophenol to 2.11 according to the

literature procedure on 100 g-scale in 85% yield (Scheme 2.3).40 We have cross-

coupled 2.11 with trimethylsilylacetylene in yields up to 85%,1 however, larger

scale reactions tended to give lower yields and we had difficulties to reproduce

previous results. This is most likely due to the low boiling point of

38

Scheme 2.1 Synthesis of acetylene 2.10: (i) 1. Zn, Me2SiCl2, DMA, (CH2Cl)2, 75˚C, 2. AcCl, 75˚C, 81%; (ii) Pd(PPh3)2Cl2, CuI, trimethylsilylacetylene, iPr2EtN, THF, 77%; (iii) TBAF, AcOH, Ac2O, THF, 0˚C, 97%.


trimethylsilylacetylene (53ºC), compared to the temperature required for the cross-

coupling (refluxing THF, 66ºC). This problem was overcome by using the higher

boiling (triisopropylsilyl)acetylene for the Sonogashira cross-coupling, followed by

deprotection of the acetylene by TBAF.41 This highly reproducible procedure gave

4.6 g of 2.13 in 83% yield over two steps.

Acetylene 2.13 was conveniently cross-coupled with 2.14 to 2.1B in 84% yield. All

attempts to replace the tert-butyl protecting group by an acetyl protecting group

with boron tribromide and acetyl chloride failed: 2.1A could not be separated from

the side products that were formed. However, a modification of the bromine

catalyzed reaction described by Mayor et al.41 gave the desired compound 2.1A. A

drawback of this method is the low reproducibility: some of the attempts resulted

in insoluble material only (most likely disulfides). For this reason we chose to

apply this reaction only on quantities up to 100 mg. Larger amounts were obtained

39

Scheme 2.2 Syntheses of the cross-conjugated anthraquinone-based compounds 2.1A-2.3: (i) Pd(PPh3)2Cl2, CuI, iPr2NH, THF, reflux; (ii) Br2, AcCl, AcOH, CHCl3.

Scheme 2.3 Synthesis of acetylene 2.13: (i) tBuCl, AlCl3, 85%; (ii) Pd(PPh3)2Cl2, CuI, triisopropylsilylacetylene, iPr2NH, THF, reflux, 99%; (iii) TBAF, THF, 0˚C, 84%.

Chapter 2

by combining several batches, after the reaction and before the purification by

column chromatography, with an average yield of 46%.

Asymmetric compound 2.2A was synthesized by similar methods: only 1.1

equivalent of 2.13 was used in the cross-coupling with 2.14, to obtain a mixture of

products (30% unreacted 2.14, 45% asymmetric product, 25% 2.1B), from which

the asymmetric product was isolated by column chromatography in 38%. This was

then cross-coupled to phenylacetylene and 2.2B was obtained in 71% yield.

Conversion of the tert-butyl group into an acetyl group by catalytic amounts of

bromine resulted in 2.2B in 83% yield.

2.2.2 Linear Conjugated Molecular Wires

To compare the properties of the cross-conjugated anthraquinone with its linear

conjugated, though unstable hydroquinone, we decided to provide this

hydroquinone with an acetyl or methyl protecting group. The synthesis of 2,6-

dibromo-9,10-diacetoxyanthracene (2.15) from 2.14 and Sonogashira cross-

couplings with this compound were described in the aforementioned article of

Leventis et al.35 The anthraquinone was reduced by zinc powder to the

hydroquinone, which then formed the bisacetyl ester upon reaction with acetic

anhydride, and 2.15 was isolated in 81% (Scheme 2.4).

40

Scheme 2.4 Syntheses of the linear conjugated anthracene-based compounds 2.4A-2.6A: (i) Zn, NaOAc, Ac2O, reflux, 81%; (ii) 1. Na2S2O4, Bu4NBr, CH2Cl2, H2O, 2. NaOH, 3. CH3I, 24%; (iii) 1. NaBH4, MeOH, toluene, 2. HCl, H2O, 3. NaBH4, iPrOH, reflux, 18%; (iv) 2.13, Pd(PPh3)2Cl2, CuI, iPr2NH, THF, reflux; (v) Br2, AcCl, AcOH, CHCl3; (vi) BBr3, AcCl, CHCl3, toluene.


A Sonogashira cross-coupling with 2.13 gave 2.4B in 75% yield and the tert-butyl

thioethers were converted into acetyl thioesters (2.4A) by the bromine catalyzed

reaction in 27% yield, following the same strategy as for the anthraquinone

compounds 2.1A and 2.2A.42,43

Anthraquinone 2.14 was also reduced to its hydroquinone by sodium dithionite36

and then, after deprotonation, trapped by iodomethane as bismethyl ether 2.16,

which was isolated in 24% yield. Compound 2.16 was then cross-coupled with

2.13, resulting in 2.5B in 56% yield, which was converted into thioester 2.5A in

43% yield. We found that the 1H NMR spectra of compound 2.5B changed upon

time when the solution was exposed to light (on air). The peak at 4.15 ppm had

disappeared after 3 days and a new peak at 4.0 ppm was found instead. After 13

days the peak at 4.0 ppm had shifted to 3.5 ppm. In both solutions we found

signals of 2.1B, together with other (small) peaks. The observed changes could be

attributed to a [4 + 4] cycloaddition to form the dimer of 2.5B (Scheme 2.5), which

can be oxidized to 2.1B, as reported for 2,3-ethynyl-9,10-dimethoxyanthracenes.44

We have synthesized the parent anthracene wire 2.6A as linear conjugated

analogue to 2.1A, to enable the formation of densely packed self-assembled

monolayers (which could be hindered by the acetyl or methoxy groups of 2.4A

and 2.5A), see Chapter 5. Anthraquinone 2.14 was reduced with sodium

borohydride to 2,6-dibromoanthracene (2.17) according to literature

procedures.45,46 After several unsuccessful or low-yielding attempts, the best result

was obtained by addition of toluene as a co-solvent in the first step of the reaction

and 2.17 was isolated in 18%. The cross-coupling with 2.13 to 2.6B, and

subsequent conversion to 2.6A by boron tribromide and acetyl chloride47 went

smoothly (80% and 61% yield respectively).

41

Scheme 2.5 Proposed structure for the photochemically formed dimer of 2.5B and its subsequent decomposition to 2.1B

Chapter 2

2.2.3 A Molecular Wire with Broken Conjugation

We completed our series of anthracene-based molecules with different conjugation

patterns by preparing a molecular wire of which the π-conjugation is broken:

molecule 2.7A consists of two π-conjugated parts that are separated by sp3

hybridized carbon atoms. The dihydroanthracene core of this molecule can be

obtained from a reduction of anthraquinone 2.14. Many common reducing agents

result in anthracenes as described in the previous section. However, the reduction

with red phosphorus, iodine, and aqueous hydroiodic acid in a sealed ampule was

reported to yield the corresponding dihydroanthracene from chloro substituted

anthraquinones.48,49 We have used these conditions to obtain 2.18 in 58% yield

(Scheme 2.6), contaminated with 2-bromo-6-diodo-9,10-dihydroanthracene

(~20%). Another side product was debrominated 9,10-dihydroanthracene, which

was removed by recrystallization. Attempts at the synthesis of 2.18 with red

phosphorus and aqueous hydroiodic acid in refluxing acetic acid50 resulted in

larger amounts of 2-bromo-6-iodo-9,10-dihydroanthracene (35-50%) in the

recrystallized product. Kwon et al. have reported the reduction of 2.14 to 2.18 by

hydroiodic acid and hypophosphorous acid in acetic acid in 50% yield.51 However,

with identical reagents, but slightly different concentrations, a high yielding

synthesis of anthracene 2.17 from 2.14 was reported.52,53

A Sonogashira cross-coupling of 2.18 and 2.13 under the conditions as used for

the syntheses of 2.1B-2.6B, gave only 16% conversion to 2.7B (the crude product

contained 36% 2.18 and 47% monosubstituted product). This is probably due to

deactivation of the C-Br bonds of 2.18 towards the oxidative insertion of the

Pd0(PPh3)2 catalyst by the two CH2 substituents of the phenyl rings.33 Replacing the

solvent (17% diisopropylamine in THF) by pure triethylamine improved the

conversion to 33% 2.7B (with only 16% 2.18 and 50% monosubstituted product).

Compound 2.7B was isolated from this mixture in 25% yield. The reaction of 2.7B

with boron tribromide and acetyl chloride to 2.7A gave no problems. However,

42

Scheme 2.6 Synthesis of dihydroanthracene-wire 2.7A: (i) Pred, I2, HI, 135˚C, 58%; (ii) 2.13, Pd(PPh3)2Cl2, CuI, Et3N, THF, reflux, 25%; (iii) BBr3, AcCl, CHCl3, toluene, 45%.


during the purification on a silica gel column, part of the material was converted

into 2.6A, hence 2.7A was obtained in only 47% yield.

2.3 Optical Properties

2.3.1 UV-Vis Absorption Spectroscopy

We have measured the UV-Vis absorption spectra of the different molecular wires

discussed in this chapter. Since the tert-butyl protected thiols (#B) have a higher

solubility, higher chemical stability, and higher similarity with thiol than the acetyl-

protected thiols (#A), we have used the tert-butyl protected thiols in our optical

studies. The UV-Vis absorption spectra are given in Figure 2.6. Spectra of 2.2B

and 2.3 are not shown: their shapes are identical to that of 2.1B with blue-shifts of

3 and 6 nm respectively. This means that each (donating) thioether group gives rise

to a slight decrease of the optical HOMO-LUMO gap. Compounds 2.4B, 2.5B,

and 2.6B have absorption spectra of similar shape. The absorption spectrum of

2.4B is red-shifted by 6-14 nm compared to spectrum 2.6B (the parent anthracene

wire), due to its acetoxy groups at the anthracene core. The stronger donating

methoxy groups of compound 2.5B result in a larger shift of 10-26 nm. Whereas

the absorption of compounds 2.1B-2.6B exceeds 420 nm, the absorption of 2.7B

ends abruptly around 335 nm, showing clearly that the molecule is divided in two

small chromophores (phenyl-ethynyl-phenyl), that have an absorption spectrum

very similar to that of compound 4.1B (diStBu-OPE2, see Chapter 4). The optical

HOMO-LUMO gaps as determined from the onsets of the absorption spectra are

43

Figure 2.6 UV-Vis absorption spectra of compounds 2.1B (blue), 2.7B (dark red), 2.4B (black), 2.5B (green), and 2.6B (red) as 10-5 M solutions in CH2Cl2.

Chapter 2

listed in Table 2.1 (page 22). Though this gap is significantly larger for 2.7B (with

its broken conjugation) than for compounds 2.1B-2.6B, the differences between

cross-conjugated wires 2.1B-2.3 and linear conjugated wires 2.4B-2.6B are only

marginal.

To gain more insight in these UV-Vis data, we calculated the electronic spectra of

2.1, 2.6, and 2.7 with methyl protected thiols, using the semi-empirical ZindoS

method in HyperchemTM with an orbital criterion of 10 occupied and 10

unoccupied orbitals. We found a good agreement between the trends in the

electronic spectra and the experimental trends, even though the absolute values are

blue-shifted by 0.2-0.4 eV. The relevant orbitals are shown in Figure 2.7, which we

will discuss from right to left. Dihydroanthracene wire 2.7 has two nearly

degenerate HOMO orbitals, which are obtained from a symmetric and an

asymmetric combination of two parts, each of which resembles the HOMO of

OPE2 (4.1B). The same holds for the two LUMO orbitals of 2.7. The nearly

degeneracy of these HOMOs and LUMOs indicates only little electronic coupling

between both parts of the molecule, reflecting its broken conjugation. The

absorption at 318 nm is attributed to combined transitions of the HOMO-1 to

LUMO and HOMO to LUMO+1.

All relevant orbitals of linear conjugated anthracene wire 2.6 extent over the entire

molecular wire. The absorptions at 417 and 393 nm are attributed to the HOMO to

LUMO transition and the combined transitions of HOMO to LUMO and HOMO

to LUMO+1 respectively. All four orbitals given in Figure 2.7 are involved in the

strong absorption at 325 nm.

The two nearly degenerate HOMO levels of cross-conjugated anthraquinone wire

2.1 resemble those of 2.7, indicating also here little electronic coupling between

both parts. However, the LUMO level of 2.1 is located on the anthraquinone unit,

as expected, since anthraquinone is a strong acceptor. The absorption at 373 nm is

attributed to the transition of the HOMO-1 to the LUMO, whereas the absorption

at 334 nm is attributed to the HOMO to LUMO+1 transition. The broad nature of

the absorption at 373 nm (which results in the relatively low value for the HOMO-

LUMO gap as determined from the onset of that absorption) could originate from

the charge-transfer character of that absorption.54

44


An alternative explanation could be that, even though calculated to have an

oscillator strength (intensity) of zero in the gas phase, the HOMO to LUMO

transition contributes to the spectrum measured in solution. We note that the

calculated energy difference between the HOMO and LUMO levels of 2.1 and 2.6

differs only 60 meV, in agreement with the nearly identical onsets of both UV-Vis

absorption spectra. It is known that this optoelectronic HOMO-LUMO gap does

not clearly distinguish the difference in electronic properties between cross-

conjugated and linear conjugated molecules, especially if the cross-conjugated

molecule has both strong electron donating and electron accepting groups.55,56

45

Figure 2.8 Excitation (dotted) and emission (solid) spectra of 2.1B (blue), 2.2B (green) and 2.3 (red) as 10-6 M solutions in CH2Cl2 and of 2.4B (black) as 10-8 M solution in CH2Cl2.. The photo in the inset shows 10-5 M solutions of 2.1B (left flask) and 2.4B (right flask) upon irradiation with a 365 nm UV lamp.

Figure 2.7 ZindoS-calculated orbitals of 2.1, 2.6, and 2.7 (all with methyl-protected thiols), that are involved in the electronic transitions corresponding to the measured absorptions.

Chapter 2

2.3.2 Fluorescence Spectroscopy

A larger difference between cross-conjugated wires 2.1B-2.3 and linear conjugated

wire 2.4B was observed in the fluorescence measurements. We observed the strong

fluorescence of compound 2.4B already during its synthesis: a solution of the

yellow compound appeared as dark blue. After measuring its fluorescence spectra

(excitation and emission) and comparing these with those of 2.1B-2.3 (Figure 2.8),

we measured fivefold higher intensity for 2.4B using as solution that was diluted

hundred times more. Thus, its fluorescence is about 500 times stronger than that of

the anthraquinone wires. This is also shown by the photo in the inset of Figure 2.8,

which shows solutions 2.1B and 2.4B under irradiation with a 365 nm UV-lamp:

2.4B (right flask) emits blue light, whereas no strong emission from 2.1B is visible.

Even though the fluorescence intensity of anthraquinone compounds 2.1B-2.3 is

much lower compared to anthracene compound 2.4B, the spectra of especially

2.1B and 2.2B show a very large Stokes shift, caused by the large polarization

differences between the excited state and the ground state of these molecules. This

effect was the main emphasis of the aforementioned study of Leventis et al.35 The

fluorescence lifetime of 2.1B was found to be 706 ps by time resolved

photoluminescence measurements,57 which is in the same order as that of

anthracene wire 2.6B (1.78 ns), excluding the possibility that the measured signals

arise from phosphorescence.

2.4 Redox-Switching of the Anthraquinone WireAnthraquinone compound 2.1 is designed as a redox switch: anthraquinone can be

reduced to its hydroquinone, which turns the cross-conjugated wire 2.1 into its

linear conjugated analogue (see Figure 2.1) and vice versa. This section presents the

measurements that prove this switching behavior.

2.4.1 Cyclic Voltammetry and DPV

We have measured cyclic voltammograms of compounds 2.1B, 2.3, 2.4B, 2.14,

and parent 9,10-anthraquinone in ODCB/acetonitrile (4:1), using 0.1 M Bu4NPF6

as the electrolyte in a three electrode cell, with platinum working and counter

electrodes and a silver wire as reference electrode. Contrary to compound 2.4B, all

46


anthraquinone-containing compounds showed two reversible reductions; the

representative cyclic voltammogram of 2.1B is shown in Figure 2.9. First the

anthraquinone is reduced to the semiquinone anion radical and then to the

hydroquinone dianion (see inset Figure 2.9). With the reversibility of both

reductions, an important requirement of our switch is fulfilled.

We have used Differential Pulse Voltammetry (DPV) to compare the positions of

these reductions and added ferrocene (Fc) as an internal reference (Fc/Fc+ = 0.64

V vs. SHE). The first reduction appears at -1.24 V (vs. Fc/Fc+) for 2.1B and at

-1.25 V, -1.24 V and -1.43 V, for 2.3, 2.14, and anthraquinone respectively. The

second reduction is -similar to the first reduction- nearly identical for compounds

2.1B, 2.3, and 2.14 (-1.80 V, -1.79 V, and -1.79 V) and significantly more negative

for anthraquinone (-2.00 V). These results indicate that the positions of the redox

waves are influenced by substitution at the 2- and 6-positions of the anthraquinone,

but that the identity of these substituents is less important: the reduction is

localized at the anthraquinone unit. These results are very promising for the

functionality of our anthraquinone-based redox-switch inside a junction, i.e. with

its thiols attached to gold electrodes.

47

Figure 2.9 Cyclic Voltammogram (left) of 2.1B in ODCB/acetonitrile (the inset shows the redox processes to which the waves in the spectrum are attributed) and DPV (right) of 9,10-anthraquinone (black), 2.1B (blue), 2.3(red), and 2.14 (green) solutions in ODCB/acetonitrile, to which ferrocene was added.

Chapter 2

2.4.2 Spectroelectrochemistry

In the electrochemical measurement we observed a color change of the solution of

2.1B from yellow to red. This change of color was measured by

spectroelectrochemistry: UV-Vis absorption spectra were measured while changing

the potential of the solution. The spectrum measured at 0 V vs. SCE (+0.24 V vs.

SHE; -0.40 vs. Fc/Fc+; see Figure 2.10, red line) was identical to the spectrum

measured in CH2Cl2 without electrochemical control (Figure 2.6, blue line). When

the potential was set at -1.6 V vs. SCE (-2.0 V vs. Fc/Fc+), new absorptions around

460 and 670 nm appeared, which are attributed to the hydroquinone dianion.58 The

original spectrum was obtained again after setting the potential back to 0 V (the

increased intensity between 300 and 450 nm is attributed to evaporation of the

solvent over time).Thus, spectroelectrochemical experiments gave additional prove

for the reversible switching of our anthraquinone wire.

2.4.3 Chemical reduction and oxidation

We have investigated chemical reduction of the anthraquinone switch as an

alternative for electrochemical reduction. Chemical reduction is of interest for

applications in a junction with a liquid cell, but without electrodes and electrolyte

solution, which complicate the experimental setup and could give rise to leakage

currents in electrical measurements. The use of metals (like zinc) or sulfur-

48

Figure 2.10 Absorption and differential absorption spectra of 2.1B in ODCB/acetonitrile 4:1 at a potential of 0 V (vs SCE) (red), -1.6 V (blue), and back at 0 V (green).


containing reducing agents (like Na2S2O4) is not desired for chemical reduction of

the anthraquinone switch inside a junction, since these reducing agents are

heterogeneous (they do not dissolve) or could modify the electrode material.

Amines are better candidates for this chemical reduction. Although most amines

are not strong enough to reduce anthraquinones,59 tetrakis(dimethylamino)ethylene

(TDAE, see inset Figure 2.11) is an exception. This electron-rich amine easily

releases two electrons to form its dication, in which the charges are highly

delocalized. TDAE is known to have a reducing power comparable to zinc,60,61 and

since zinc can be used to reduce anthraquinones (see for example the synthesis of

2.15), TDAE is expected reduce the anthraquinone-based switch to its dianion

state.

We have added TDAE to a solution of 2.1B in CDCl3 in a sealed NMR tube and

measured a 1H NMR spectrum different from that of the starting compound, with

broad signals in the aromatic region (Figure 2.11). This broadening could be

caused by the formation of paramagnetic species in the sample or exchange

processes (for instance proton exchange with the solvent). The signals became

slightly sharper after two hours and did not change in the next two days. Opening

49

Figure 2.11 1H NMR spectra (8.65-7.35 ppm) of (a) anthraquinone 2.1B in CDCl3, (b) 2 mM 2.1B and 18 mM TDAE in CDCl3 after 10 minutes, (c) the same solution after 150 minutes, and (d) after bubbling air through this solution (a suspension was formed). The inset shows the structure of TDAE and its oxidation.

Chapter 2

the NMR tube for about 10 seconds had no effect on the solution, however, the

spectrum of 2.1B was obtained again upon bubbling air through the solution. This

experiment shows that we can “switch” anthraquinone 2.1B with TDAE to

another state and that we can “switch” back with oxygen. Based on the reducing

power of TDAE we expect the product from the reaction between 2.1B and TDAE

to be the hydroquinone dianion of 2.1B (stabilized by the dication of TDAE).

However, we cannot exclude the possibility that the semiquinone radical anion

state of 2.1B is formed instead of the hydroquinone dianion. Attempts to further

analyze the product of the reaction of TDAE with anthraquinone 2.1B by UV-Vis

spectroscopy were not successful: the UV-Vis absorption spectra that were obtained

upon dilution of the solutions used in the NMR experiments were a superposition

of the spectrum of 2.1B and that of TDAE. This could either be due to trace

amounts of oxygen in the dried and degassed CHCl3 used for the dilution or to

decreased stability of the salt at low concentrations. Even though the product was

not identified and the use of an excess of TDAE and the absence of oxygen appear

to be important conditions for the reduction of the anthraquinone, the reversible

chemical switching as observed in the NMR experiments is still promising for

applications in electrical junctions.

2.5 Energy LevelsKnowing the positions of the energy levels of our molecules with respect to the

electrodes is useful for the interpretation of conductance measurements. In Table

2.1 we have listed the values of the HOMO-LUMO gap as determined form the

onsets of the UV-Vis spectra (section 2.3.1). In order to obtain information about

the positions of the energy levels, we have performed semi-empirical calculations,

using the AM1-RHF method for structure optimization on the molecules with

methyl-protected thiols. Table 2.1 shows the obtained lengths of the molecules and

energies of the HOMO levels (EHOMO). These calculations are known to give

accurate trends of EHOMO for a series of molecules, however the absolute values

from these calculations are not reliable. Therefore, we have determined the EHOMO

of 2.3 by an Ultraviolet Photoelectron Spectroscopy (UPS) measurement. In this

measurement UV photons from a Helium lamp (21.2 eV) hit a surface, from which

electrons are released with a kinetic energy (Ekin) which is 21.2 eV minus the

binding energy (Ebinding). Thus, Ebinding can be determined from measuring Ekin.

50


Table 2.1 Molecular Length and Energy Levels.

Wire HOMO-LUMO

gap (eV)a

Lengthb calculated c

(Å)

EHOMO calculated c

(eV)

EHOMO UPS(eV)

EHOMO corrected d

(eV)

ELUMO EC e

(eV)

2.1 2.88 24.25 -8.193 -6.03 -3.56

2.2 2.93 23.66 -8.199 -6.04

2.3 2.96 23.07 -9.045* -6.1±0.1 -6.10 -3.55

2.4 2.79 24.23 -7.553 -5.39

2.5 2.70 24.26 -7.516 -5.36

2.6 2.90 24.20 -7.900 -5.74

2.7 3.75 24.06 -8.041 -5.88

a. Determined from the onsets of the UV-Vis spectra of the 2.#B compounds in CH2Cl2.b. The distance from S- to S-atom (we used the outer H-atoms in absence of S-atoms for 2.2B and 2.3).c. HyperchemTM Release 7.52 for Windows Molecular Modeling Systems. Structures were optimized using the

AM1-RHF method. We used methyl-substituted thiols in the calculations.d. All levels were shifted by +2.16 eV to get agreement with the HOMO level as determined by the UPS

measurement.e. determined from electrochemical measurements (DPV), with EHOMO of ferrocene at -4.8 eV.62

* This value is much lower than EHOMO of 2.1 and 2.2, probably because this molecule is symmetric in the calculations, due to the lack of substituted thiols that bend out of the plane. When comparing the HOMO-LUMO gap and ELUMO from solution measurements on 2.1B and 2.3, EHOMO of 2.3 is expected to be only 70 meV lower in energy than that of 2.1B.

51

Figure 2.12 UPS spectra of ~20 nm thermally evaporated 2.3 on a gold substrate (solid line) and of 150 nm gold on mica (dotted line) at a bias of -4 V.

Chapter 2

We have thermally evaporated a layer of about 20 nm of 2.3 onto a substrate of

150 nm gold on mica. The UPS spectrum was recorded at a bias of -4 V, to

accelerate the electrons between sample and detector. For comparison we also

measured the gold substrate without evaporated compound (without cleaning the

substrate prior to the measurement). Both UPS spectra are given in Figure 2.12.

The energy level of the HOMO (EHOMO) of 2.3 is determined by subtraction of the

width of the spectrum (i.e. the right onset minus the left onset) from the energy of

the photons, which gives EHOMO = -6.1±0.1 eV. The Fermi level of the gold layer

was determined by the same method, to give EFermi = -4.5 eV. This latter value

deviates from values measured by others,63 most likely due to adsorbed species

from the ambient on the gold surface. The value of -6.1±0.1 eV was used to adjust

the energy levels from the semi-empirical calculations (see Table 2.1). We will

discuss the alignment of our molecular levels with the electrode materials and the

implication for the electrical conductance in Chapters 4 and 5.

2.6 Crystal StructureWe obtained a crystal structure from anthraquinone wire 2.3 and found that the

molecule is nearly flat (Figure 2.13), in contrast to the regioisomer 2,7-

bis(phenylethynyl)-9,10-anthraquinone, which is bent.35 The outer phenyl rings of

2.3 are twisted only 7.26° with respect to the anthraquinone core. When we look at

the packing in the crystal structure, we find two spacing distances: there are rows

of molecules in which the phenyl-acetylene-phenyl unit of one molecule lays on

top of the anthraquinone unit of the next molecule with a distance of 3.494 Å. In

between these rows there are slides of molecules of which the phenyl-acetylene-

phenyl unit of one molecule lays on top of the phenyl-acetylene-phenyl unit of the

52

Figure 2.13 Crystal Structure of 2.3 (a and b) and its packing (c and d).


next molecule, with the much larger spacing of 10.261 Å. Especially the finding

that the molecule is nearly flat -in agreement with gas phase calculations- is of

great importance for conductance measurements, since the electronic

communication between the different parts of the conjugated molecule will be

optimal if they lay in one plane (i.e. all pz-orbitals are parallel).

2.7 ConclusionsWe have synthesized an anthraquinone-based redox switch, along with anthracene

and dihydroanthracene analogues. The conjugation pattern of these compounds

varies from cross-conjugation to linear conjugation and broken conjugation, which

is reflected by their spectroscopic properties. We have shown that the

anthraquinone-based redox switch can be reversibly switched by electrochemistry

and by chemical reduction and oxidation. With these compounds at hand, we can

start comparing the electronic transport through these molecular wires to find the

influence of the conjugation pattern on the conductance by various methods (see

Chapter 5).

53

Chapter 2

2.8 Experimental Section

2.8.1 GeneralAll reactions were performed under a nitrogen atmosphere, using oven-dried glassware (150°C)

and dry solvents (solvents for reactions towards 2.8, and 2.14-2.18 were not dried). All chemicals were purchased from Aldrich, Acros, or AlfaAesar and used as received. Diisopropylamine and

triethylamine were distilled over NaOH. Copper iodide was heated and dried under vacuum. TBAF refers to tetrabutylammonium fluoride trihydrate. Silica gel was purchased from Screening

Devices b.v. as SilicaFlash P60, with particle sizes of 40-63 μm and a pore size of 60Å. 1H and 13C NMR spectra were recorded on a Varian VXR-300 (300 MHz), a Varian AMX400

(400 MHz), or a Varian unity plus (500 MHz) at room temperature, unless depicted otherwise. Spectra were referenced to the solvent line (CDCl3: H, 7.26 ppm; C, 77.0 ppm; C2D2Cl4: H, 5.95

ppm; C, 72.5 ppm) relative to tetramethylsilane. FT-IR spectra were recorded on a Nicolet Nexus FT-IR spectrometer, using the SMART iTR for ATR measurements (diamond). Indicated solids

were measured in KBr using a Smart Collector DRIFT setup and indicated liquids were measured in the transmission mode between NaCl windows. Mass spectra were recorded on a

Thermo Scientific Orbitrap XL or on a Jeol JMS-600H. UV-Vis absorption spectra were measured on a Perkin/Elmer Lambda 900 UV-Vis-NIR

Spectrometer at 10-5 M in dichloromethane in a quartz cuvet with a pathlength of 1 cm. Fluorescence measurements were performed on a Fluorolog 3 (Jobin Yvon Horiba) in

dichloromethane, using filters of 370 and 399 nm. Time-resolved photoluminescence measurements were performed, exciting the solutions at 380 nm by a 150 fs pulsed Kerr mode

locked Ti-sapphire laser and the photoluminescence was recorded by a Hamamatsu streak camera working in synchroscan mode, with a photocathode sensitive in the visible spectral range.Cyclic Voltammetry spectra were recorded at 10 mV/s on an Autolab PGstat 100 with Pt working and counter electrodes and a Ag reference electrode. Concentrations in analyte were

mM in a mixture of o-dichlorobenzene (ODCB) and acetonitrile (4:1) containing Bu4NPF6 (0.1 M) as supporting electrolyte. Solutions were purged with nitrogen prior to the measurement.

Ferrocene was used a reference compound. For spectroelectrochemical measurements a CHI630B electrochemical analyzer and a HP8453 UV-Vis spectrometer were used. A thin cell (1

mm) was supported with a Pt gauze working electrode, a Pt wire counter electrode and a SCE reference electrode.

For the UPS measurement 20 nm 2.3 was thermally evaporated onto gold (150 nm) on mica (see Experimental Section of Chapter 3). The UPS measurement was run in a homebuilt UHV

system with a Helium lamp (50 mA, 0.58 kV, 0.2 mbar). The detector was grounded and a bias of -4 V was applied on the sample. The UPS spectrum was recorded within 10 minutes after

positioning the UV beam on the sample.

54


2.8.2 Synthesis and Analysis of the Molecular Wires (2.1-2.7)

2,6-Bis[(4-tert-butylthiophenyl)ethynyl]-9,10-anthraquinone (2.1B)

To a suspension of 2.14 (579 mg, 1.58 mmol), dichlorobis(triphenylphosphine)palladium(II)

(110 mg, 0.16 mmol), and copper iodide (34 mg, 0.18 mmol) in THF (65 mL) were added

diisopropylamine (13 mL) and 2.13 (748 mg, 3.93 mmol). The reaction mixture was refluxed for 21 hours and poured into water (400 mL). This was extracted with CH2Cl2

(4 x 200 mL) and the

combined organic layers were washed with water (4 x 400 mL) and brine (400 mL), dried over Na2SO4, filtered, and concentrated. The crude solid was preadsorbed onto silica and purified by

column chromatography twice (silica gel, CH2Cl2; silica gel, CH2Cl2/heptane 1:1). The obtained solid was recrystallized form toluene to yield 627 mg (1.07 mmol, 84%) of the title compound as

a yellow solid.1H NMR (400 MHz, CDCl3): 8.45 (d, δ J = 1.7, 2H), 8.33 (d, J = 8.1, 2H), 7.92 (dd, J = 8.1, 1.7,

2H), 7.60-7.50 (m, 8H), 1.32 (s, 18H). 13C NMR (75 MHz, CDCl3): 181.92, 137.28, 136.56,δ 134.58, 133.50, 132.27, 131.74, 130.33, 129.61, 127.53, 122.48, 93.95, 89.35, 46.72, 31.02. IR

(cm-1): 2974, 2863, 2214, 1671, 1593, 1586, 1473, 1365, 1324, 1301, 1276, 1165, 982, 916, 880, 847, 835, 740, 709. HRMS (APCI) calculated for [M+H]+ 585.1916, found 585.1870. Calcd for

C38H32O2S2: C, 78.05; H, 5.52; S, 10.97. Found: C, 78.42; H, 5.56; S, 10.88.

2,6-Bis[(4-acetylthiophenyl)ethynyl]-9,10-anthraquinone (2.1A)

Chloroform (18 mL) was added to 2.1B (102 mg,

0.17 mmol) and heated for a moment to obtain a yellow solution, to which acetyl chloride (5.5 mL)

was added. A solution of bromine (0.2-0.5 mL, 0.3 M) in acetyl chloride/acetic acid (1:1) was added dropwise in the dark. The reaction mixture

was stirred for 2-4 hours and poured into 250 mL ice water and stirred for 1 hour. The mixture was extracted with CH2Cl2 (3 x 200 mL), dried over Na2SO4, filtered, and concentrated. This

reaction was repeated 3 times. The combined yellow solids (0.30 g) were preadsorbed onto silica and purified by column chromatography (silica gel, CH2Cl2) to yield 181 mg (0.324 mmol, 46%)

of the title compound as a yellow solid.1H NMR (500 MHz, CDCl3): 8.45 (d, δ J = 1.2, 2H), 8.33 (d, J = 8.0, 2H), 7.92 (dd, J = 8.0, 1.7,

2H), 7.62 (d, J = 8.3, 4H), 7.45 (d, J = 8.3, 4H), 2.46 (s, 6H). 13C NMR (125 MHz, CHCl3): δ 193.16, 181.87, 136.63, 134.31, 133.50, 132.42, 132.35, 130.41, 129.45, 129.27, 127.54, 123.37,

93.60, 89.45, 30.36. IR (cm-1): 3065, 2923, 2219, 1702, 1670, 1589, 1324, 1303, 1276, 1245, 1121, 1101, 1090, 981, 957, 919, 881, 863, 827, 741, 711. HRMS (APCI) calculated for [M+H]+

557.0876, found 557.0834. Calcd for C34H20O4S2: C, 73.36; H, 3.62; S, 11.52. Found: C, 72.96; H, 3.72; S, 11.32.

2-bromo-6-[(4-tert-butylthiophenyl)ethynyl]-9,10-anthraquinone


55

Chapter 2

(75.9 mg, 0.108 mmol), and copper iodide (27.7 mg, 0.145

mmol) in THF (80 mL) were added diisopropylamine (12 mL) and 2.13 (422 mg, 2.22 mmol). The reaction mixture was

refluxed for 22 hours and all volatiles were removed. The crude solid was dissolved in CH2Cl2

(400 mL), washed with water (2 x 200 mL) and brine (200 mL),

dried over Na2SO4, filtered, and preadsorbed onto silica. This reaction was repeated and the combined material was purified by column chromatography twice (silica gel, CH 2Cl2; silica gel,

CH2Cl2/heptane 2:3) to afford 737 mg (1.55 mmol, 38%) of the title compound as a yellow solid.1H NMR (400 MHz, CDCl3): 8.45 (d, δ J = 1.9, 1H), 8.44 (d, J = 1.4, 1H), 8.30 (d, J = 8.0, 1H),

8.19 (d, J = 8.3, 1H), 7.93 (ddd, J = 9.6, 8.2, 1.8, 2H), 7.61-7.50 (m, 4H), 1.32 (s, 9H). 13C NMR (100 MHz, CDCl3): 181.83, 181.30, 137.27, 137.24, 136.65, 134.64, 134.53, 133.23, 131.99,δ

131.94, 131.74, 130.31, 130.00, 129.76, 129.09, 127.56, 122.40, 94.11, 89.25, 46.72, 31.01. IR (KBr, cm-1): 3322, 3065, 2977, 2961, 2865, 2215, 1672, 1599, 1580, 1327, 1314, 1305, 1283,

1167, 980, 865, 850, 832, 737, 710, 546, 540.

2-[(4-tert-butylthiophenyl)ethynyl]-6-(phenylethynyl)-9,10-anthraquinone (2.2B)

To a suspension of 2-bromo-6-[(4-tert-butylthiophenyl)ethynyl]-9,10-anthraquinone (399 mg, 0.84 mmol), dichlorobis(triphenylphosphine)

palladium(II) (66 mg, 0.093 mmol), and copper iodide (21 mg, 0.11 mmol) in THF (42 mL) were added diisopropylamine (8 mL) and phenylacetylene

(161 mg, 1.58 mmol). The reaction mixture was refluxed for 20 hours and all volatiles were removed. The residue was dissolved in 300 mL CH2Cl2, washed with water (3 x 200 mL), dried

over Na2SO4, filtered, and concentrated. The crude solid was preadsorbed onto silica and purified by column chromatography twice (silica gel, CH2Cl2; silica gel, CH2Cl2/heptane 1:1,

gradually increasing to 3:2). The obtained solid was recrystallized form toluene to yield 296 mg (0.60 mmol, 71%) of the title compound as a yellow solid.1H NMR (400 MHz, CDCl3): 8.44 (d, δ J = 1.6, 2H), 8.32 (dd, J = 8.0, 1.8, 2H), 7.91 (dt, J = 8.0, 1.7, 2H), 7.62-7.51 (m, 6H), 7.44 -7.37 (m, 3H), 1.32 (s, 9H). 13C NMR (125 MHz, CDCl3):

181.93, 137.27, 136.55, 136.52, 134.57, 133.52, 133.48, 132.30, 132.15, 131.91, 131.74,δ 130.31, 130.29, 129.88, 129.56, 129.21, 128.53, 127.51, 127.49, 122.50, 122.23, 94.58, 93.90,

89.37, 88.01, 46.71, 31.02. IR (KBr, cm-1): 3346, 2980, 2958, 2937, 2920, 2895, 2861, 2217, 1681, 1598, 1336, 1304, 1169, 922, 856, 835, 756, 740, 712, 691, 579, 544, 533. HRMS (APCI)

calculated for [M+H]+ 497.15698, found 497.15661. Calcd for C34H22O2S: C, 83.23; H, 4.87; S, 6.46. Found: C, 81.75; H, 4.82; S, 6.38.

2-[(4-acetylthiophenyl)ethynyl]-6-(phenylethynyl)-9,10-anthraquinone (2.2A)

Chloroform (17 mL) was added to 2.2B (100 mg, 0.20 mmol) and stirred to obtain a yellow solution, to which

acetyl chloride (5.0 mL) was added. A solution of bromine (0.2 mL, 0.3 M) in acetyl chloride/acetic acid (1:1) was added dropwise in the dark.

The reaction mixture was stirred for 2.5 hours and poured into 250 mL ice water and stirred for 1 hour. The mixture was extracted with CH2Cl2 (3 x 150 mL), dried over Na2SO4, filtered, and

concentrated. This reaction was repeated 2 times. The combined yellow solids (0.26 g) were

56


preadsorbed onto silica and purified by column chromatography (silica gel, CH2Cl2) to yield 233

mg (0.483 mmol, 83%) of the title compound as a yellow solid.1H NMR (400 MHz, CDCl3): 8.45 (dd, δ J = 1.2, 0.5, 2H), 8.32 (dd, J = 8.0, 2.3, 2H), 7.92 (dd, J = 8.1, 1.7, 2H), 7.64-7.57 (m, 4H), 7.46-7.44 (m, 2H), 7.43-7.38 (m, 3H), 2.46 (s, 3H). 13C NMR (125 MHz, CDCl3): 193.15, 181.92, 181.87, 136.57, 136.55, 134.29, 133.49, 133.45, 132.41,δ

132.36, 132.12, 131.90, 130.38, 130.28, 129.87, 129.38, 129.25, 129.21, 128.52, 127.50, 123.37, 122.21, 94.58, 93.55, 89.47, 88.01, 30.35. IR (cm-1): 3060, 2923, 2211, 1697, 1671, 1584, 1323,

1300, 1274, 1131, 983, 950, 915, 881, 857, 827, 754, 741, 710, 687, 624. HRMS (APCI) calculated for [M+H]+ 483.10494, found 483.10485. Calcd for C32H18O3S: C, 79.65; H, 3.76; S,

6.64. Found: C, 78.82; H, 3.99; S, 6.19.

2,6-Bis(phenylethynyl)-9,10-anthraquinone (2.3)

This compound was prepared by a modification of literature

methods.35 To a suspension of 2.14 (597 mg, 1.63 mmol), dichlorobis(triphenylphosphine)palladium(II) (113 mg, 0.16

mmol), and copper iodide (36.4 mg, 0.19 mmol) in THF (80 mL) were added diisopropylamine (12 mL) and phenylacetylene (410 mg, 4.02 mmol). The

reaction mixture was refluxed for 21 hours and all volatiles were removed. The residue was suspended in 800 mL CH2Cl2 and washed with water (3 x 200 mL), dried over Na2SO4, filtered,

and concentrated. The crude solid was preadsorbed onto silica and purified by column chromatography twice (silica gel, CH2Cl2; silica gel, CH2Cl2/heptane 1:1, gradually increasing to

2:1). The obtained solid was recrystallized form toluene to yield 373 mg (0.91 mmol, 56%) of the title compound as dark yellow needles.1H NMR (500 MHz, CDCl3): 8.47 (s, 2H), 8.34 (d, δ J = 8.0, 2H), 7.94 (d, J = 8.0, 2H), 7.62 (d, J = 3.4, 4H), 7.43 (bd, J = 2.4, 6H). 13C NMR (125 MHz, CDCl3): 181.98, 136.53, 133.50,δ

132.17, 131.90, 130.28, 129.85, 129.21, 128.53, 127.49, 122.23, 94.53, 88.02. IR (cm -1): 3315, 3067, 2205, 1667, 1586, 1444, 1323, 1299, 1272, 1249, 1177, 984, 910, 880, 847, 757, 742, 708,

681, 660. HRMS (APCI) calculated for [M+H]+ 409.12231, found 409.12279. Calcd for C30H16O2: C, 88.22; H, 3.95. Found: C, 88.22; H, 3.86.

2,6-Bis[(4-tert-butylthiophenyl)ethynyl]-9,10-diacetoxyanthracene (2.4B)

To a suspension of 2.15 (0.474 g, 1.05 mmol), dichlorobis(triphenylphosphine)palladium(II)

(72.2 mg, 0.103 mmol) and copper iodide (57.5 mg, 0.302 mmol) in THF (80 mL) were added

2.13 (0.640 g, 3.36 mmol) and diisopropylamine (16 mL). The reaction mixture was refluxed for 24 hours and the solvent was removed by rotary

evaporation. The crude material was suspended in CH2Cl2 (100 mL) and poured into water (200 mL). The aqueous layer was extracted with CH2Cl2 (100 mL) and the combined organic layers

were washed with water (4 x 200 mL), dried over Na2SO4 and the solvent was removed by rotary evaporation. The crude product was purified by column chromatography (silica gel, CH2Cl2) to

give 0.629 g of a yellow-brown solid. This was dissolved in hot chloroform (30 mL) and upon addition of hexane (30 mL) a yellow precipitate was formed. The solution was cooled, the

precipitate was filtered off, washed with hexane and dried to afford 532 mg (0.79 mmol, 75 %) of

57

Chapter 2

the title compound as a yellow solid. 1H NMR (CDCl3, 400 MHz): δ 8.12 (s, 2H), 7.91 (d, J = 8.8 Hz, 2H), 7.59 (d, J = 8.8 Hz, 2H), 7.57-7.54 (m, 8H), 2.69 (s, 6H), 1.32 (s, 18H). 13C NMR (CDCl3, 100 MHz): δ 169.3, 140.2,

137.3, 133.8, 131.6, 129.0, 125.4, 124.4, 123.6, 123.2, 122.2, 121.5, 91.1, 91.0, 46.6, 31.0, 20.84. IR (KBr, cm-1): 2972, 2959, 2922, 2897, 2862, 2210, 1761, 1618, 1364, 1192, 1158, 1045, 829.

MS (EI): m/z 670 (M+, 35 %). Calcd for C42H38O4S2: C, 75.19; H, 5.71. Found: C, 75.20; H, 5.63.

2,6-Bis[(4-acetylthiophenyl)ethynyl]-9,10-diacetoxyanthracene (2.4A)

2.4B (100 mg, 0.20 mmol) was dissolved in

chloroform (17 mL) and acetyl chloride (5.0 mL) was added. A solution of bromine (0.2 mL, 0.3

M) in acetyl chloride/acetic acid (1:1) was added dropwise in the dark. The reaction mixture was

stirred for 1.5 hours and poured into 250 mL ice water and stirred for 1 hour. The mixture was extracted with CH2Cl2 (4 x 200 mL), dried over Na2SO4, filtered, and concentrated. The crude

material was preadsorbed onto silica and purified by column chromatography (silica gel, CH2Cl2) to yield 27 mg (0.042 mmol, 27%) of the title compound as a yellow solid.1H NMR (400 MHz, CDCl3): 8.12 (d, δ J = 0.9, 2H), 7.92 (d, J = 9.1, 2H), 7.63 (d, J = 8.4, 4H), 7.59 (dd, J = 9.0, 1.4, 2H), 7.44 (d, J = 8.4, 4H), 2.69 (s, 6H), 2.45 (s, 6H). 13C NMR (100 MHz,

C2D4Cl4): 192.36, 168.21, 138.70, 132.94, 130.96, 127.77, 127.26, 124.05, 122.82, 122.42,δ 122.06, 120.79, 120.04, 89.79, 89.67, 29.10, 19.58. IR (cm-1): 2921, 2851, 2212, 1749, 1689,

1360, 1206, 1161, 1130, 1114, 1046, 1004, 954, 885, 826, 811, 790, 741, 625. HRMS (APCI) calculated for [M+H]+ 643.12436, found 643.12429.

2,6-Bis[(4-tert-butylthiophenyl)ethynyl]-9,10-dimethoxyanthracene (2.5B)


(58.0 mg, 0.083 mmol), and copper iodide (19.2 mg, 0.101 mmol) in THF (40 mL) were added

diisopropylamine (8 mL) and 2.13 (402 mg, 2.11 mmol). The reaction mixture was refluxed for 16 hours and poured into water (200 mL). This was extracted with CH2Cl2

(4 x 100 mL) and the

combined organic layers were washed with water (6 x 100 mL), dried over Na2SO4, filtered, and concentrated. The crude solid was preadsorbed onto silica and purified by column

chromatography twice (silica gel, CH2Cl2; silica gel, CH2Cl2/heptane 1:1). The obtained solid was recrystallized form toluene to yield 276 mg (0.45 mmol, 56%) of the title compound as a

yellow solid. 1H NMR (400 MHz, CDCl3): 8.49 (s, 2H), 8.27 (d, δ J = 8.9, 2H), 7.61-7.53 (m, 10H), 4.15 (s, 6H), 1.32 (s, 18H). 13C NMR (125 MHz, CDCl3): 148.48, 137.30, 133.49,δ

131.58, 127.90, 126.55, 125.16, 124.32, 123.50, 123.01, 120.31, 91.66, 90.27, 63.68, 46.57, 31.00. IR (cm-1): 3072, 2957, 2938, 2838, 2208, 1617, 1487, 1450, 1359, 1302, 1162, 1126, 1059,

953, 902, 832, 718. HRMS (APCI) calculated for [M+H]+ 615.23860, found 615.23833. Calcd for C40H38O2S2: C, 78.14; H, 6.23; S, 10.43. Found: C, 78.77; H, 6.21; S, 10.21.

58


2,6-Bis[(4-acetylthiophenyl)ethynyl]-9,10-dimethoxyanthracene (2.5A)

Chloroform (20 mL) was added to 2.5B (107 mg,

0.17 mmol) and heated for a moment to obtain a yellow solution, to which acetyl chloride (5 mL)

was added. A solution of bromine (0.25 mL, 0.3 M) in acetyl chloride/acetic acid (1:1) was added dropwise in the dark. The reaction mixture was

stirred for 2-3 hours and poured into 250 mL ice water and stirred for 1 hour. The mixture was extracted with CH2Cl2 (3 x 150 mL), dried over Na2SO4, filtered, and concentrated. This reaction

was repeated once. The combined yellow solids (0.22 g) were preadsorbed onto silica and purified by column chromatography (silica gel, CH2Cl2) to yield 78 mg (0.13 mmol, 43%) of the

title compound as a yellow solid.1H NMR (400 MHz, CDCl3): 8.49 (s, 2H), 8.27 (d, δ J = 9.0, 2H), 7.65 (d, J = 8.0, 4H), 7.57 (d,

J = 9.0, 2H), 7.44 (d, J = 8.0, 4H), 4.16 (s, 6H), 2.46 (s, 6H). 13C NMR (125 MHz, CDCl3): δ 193.44, 148.52, 134.26, 132.26, 128.25, 127.88, 126.68, 125.17, 124.40, 124.34, 123.03, 120.20,

91.83, 90.04, 63.69, 30.32. IR (cm -1): 2997, 2940, 2834, 2209, 1694, 1443, 1354, 1301, 1127, 1060, 983, 962, 881, 828, 810, 714, 627. HRMS (APCI) calculated for [M+H]+ 587.13453,

found 587.13472. Calcd for C36H26O4S2: C, 73.70; H, 4.47; S, 10.93. Found: C, 72.13; H, 4.46; S, 10.44.

2,6-Bis[(4-tert-butylthiophenyl)ethynyl]anthracene (2.6B)


(85.2 mg , 0.121 mmol), and copper iodide (36.4 mg, 0.191 mmol) in THF (60 mL) were added

diisopropylamine (12 mL) and 2.13 (555 mg, 2.91 mmol). The reaction mixture was refluxed for 18 hours and all volatiles were removed. The residue was suspended in 150 mL CH2Cl2 and

poured into 350 mL water. The aqueous phase was extracted with CH 2Cl2 (2 x 150 mL). The combined organic layers were washed with water (3 x 200 mL), dried over Na 2SO4, filtered, and

part of the solvent was removed under reduced pressure. The concentrated solution was run over a column (silica gel, CH2Cl2). The obtained solid was recrystallized form toluene to yield 533 mg

(0.96 mmol, 80%) of the title compound as slightly green needles.1H NMR (400 MHz, CDCl3): 8.38 (s, 2H), 8.22 (s, 2H), 7.99 (d, δ J = 8.7, 2H), 7.58-7.52 (m,

10H), 1.32 (s, 18H). 13C NMR (100 MHz, CDCl3): 137.29, 133.43, 131.94, 131.55, 131.12,δ 128.43, 127.97, 126.39, 123.54, 120.31, 91.44, 90.17, 46.56, 31.00. IR (cm -1): 2960, 2939, 2919,

2893, 2958, 2211, 2163, 1918, 1619, 1486, 1474, 1454, 1395, 1365, 1279, 1170, 1154, 1098, 1015, 909, 867, 829, 797, 730, 657. HRMS (APCI) calculated for [M+H]+ 555.2175, found

555.2131. Calcd for C38H34S2: C, 82.26; H, 6.18; S, 11.56. Found: C, 82.27; H, 6.19; S, 11.43.

2,6-Bis[(4-acetylthiophenyl)ethynyl]anthracene (2.6A)


chloroform (50 mL) and toluene (50 mL) upon heating and stirring. After cooling to room

temperature acetyl chloride (10 mL) was added. While stirring, BBr3 (1 M in CH2Cl2, 15 mL, 15

59

Chapter 2

mmol) was added slowly. The reaction mixture was stirred for 5 hours and poured into ice water

(600 mL). This was extracted with CH2Cl2 (4 x 200 mL), dried over Na2SO4, filtered, and all volatiles were removed by rotary evaporation. The crude material was preadsorbed onto silica gel

and purified by column chromatography (silica gel, CH2Cl2/heptane, gradually increased from 2:1 to 4:1) yielding 174 mg (0.33 mmol, 61%) of the title compound as a dark yellow solid.1H NMR (400 MHz, CDCl3): 8.38 (s, 2H), 8.23 (s, 2H), 7.99 (d, δ J = 8.8, 2H), 7.63 (d, J = 8.2, 4H), 7.55 (d, J = 8.6, 2H), 7.44 (d, J = 8.2, 4H), 2.45 (s, 6H). 13C NMR (125 MHz, CDCl3): δ 193.42, 134.27, 132.24, 132.09, 131.59, 131.17, 128.47, 128.24, 127.96, 126.44, 124.46, 120.23, 91.63, 89.95, 30.31. IR (cm-1): 3371, 3058, 2957, 2921, 2851, 2211, 1913, 1691, 1615, 1486, 1396,

1352, 1280, 1110, 948, 908, 822, 802, 626. HRMS (APCI) calculated for [M+H]+ 527.1134, found 527.1092. Calcd for C34H22O2S2 C, 77.54; H, 4.21; S, 12.18. Found: C, 77.90; H, 5.34; S,

10.48.

2,6-Bis[(4-tert-butylthiophenyl)ethynyl]-9,10-dihydroanthracene (2.7B)

To a suspension of 2.18 (395 mg, 2.06 mmol),

dichlorobis(triphenylphosphine)palladium(II) (147 mg , 0.21 mmol), and copper iodide (55.4

mg, 0.29 mmol) in triethylamine (35 mL) was added 2.13 (937 mg, 4.93 mmol). The reaction mixture was refluxed for 16 hours and all

volatiles were removed. The resulting solid was preadsorbed onto silica and run over a plug of silica gel, eluted with CH2Cl2. The product was preadsorbed onto silica and further purified by

column chromatography (silica gel, CH2Cl2/heptane 1:2). The obtained solid was recrystallized form diethyl ether to yield 288 mg (0.52 mmol, 25%) of the title compound as a white solid.1H NMR (500 MHz, CDCl3): 7.53-7.46 (m, δ J = 8.1, 10H), 7.39 (dd, J = 7.8, 1.2, 2H), 7.29 (d, J = 7.8, 2H), 3.96 (s, 4H), 1.30 (s, 18H). 13C NMR (125 MHz, CDCl3): 137.24, 136.84, 136.37,δ

133.05, 131.44, 130.52, 129.60, 127.55, 123.76, 120.87, 90.97, 88.40, 46.47, 35.85, 30.97. IR (cm-1): 2960, 2919, 2894, 2859, 2209, 1500, 1417, 1361, 1169, 1152, 1014, 922, 829, 810, 803,

716. HRMS (APCI) calculated for [M+H]+ 557.23312, found 557.23256. Calcd for C38H36S2: C, 81.97; H, 6.52; S, 11.52. Found: C, 82.04; H, 6.53; S, 11.53.

2,6-Bis[(4-acetylthiophenyl)ethynyl]-9,10-dihydroanthracene (2.7A)

2.7B (188 mg, 0.334 mmol) was dissolved in chloroform (21 mL) and toluene (20 mL) and

acetyl chloride (4 mL) was added. While stirring, BBr3 (1 M in CH

2Cl

2, 8 mL, 8 mmol) was added

slowly. The reaction mixture was stirred for 5 hours and poured into ice water (400 mL). This was extracted with CH2Cl2 (4 x 125 mL), dried over Na2SO4, filtered, and all volatiles were

removed by rotary evaporation. The crude material was preadsorbed onto silica gel and purified by column chromatography (silica gel, CH2Cl2/heptane 2:1) yielding 83 mg (0.157 mmol, 47%)

of the title compound as a light yellow solid. 1H NMR (400 MHz, CDCl3): 7.55 (d, δ J = 8.1, 4H), 7.49 (s, 2H), 7.43-7.37 (m, 6H), 7.29 (d, J =

7.8, 2H), 3.96 (s, 4H), 2.44 (d, J = 1.0, 6H). 13C NMR (125 MHz, CDCl3): 193.50, 136.93,δ 136.35, 134.20, 132.11, 130.57, 129.64, 127.84, 127.55, 124.66, 120.71, 91.17, 88.19, 35.82,

30.27. IR (cm-1): 3057, 2926, 2859, 2209, 1705, 1498, 1415, 1396, 1124, 1109, 1100, 1089, 949,

60


920, 829, 811, 619. HRMS (APCI) calculated for [M+H]+ 529.12905, found 529.12893. Calcd

for C34H24O2S2: C, 77.24; H, 4.58; S, 12.13. Found: C, 77.25; H, 4.65; S, 12.03.

2.8.3 Synthesis and Analysis of the Acetylene Precursors (2.8-2.13)

4-Iodophenylthioacetate (2.8)

This compound was prepared according to a literature procedure.37 A solution of pipsyl chloride (5.01 g, 16.6 mmol) and N,N-dimethyl acetamide (4.6 mL, 49

mmol) in 1,2-dichloroethane (130 mL) was added to a suspension of zinc powder (3.85 g, 58.9 mmol) and dichlorodimethylsilane (7.0 mL, 58 mmol) in 1,2-dichloroethane (130

mL). The gray suspension was stirred for 2.5 hours at 70-75 °C to give a yellow-green solution. This solution was cooled to 50 °C and acetyl chloride (1.52 mL, 21.4 mmol) was added. The

mixture was stirred for 30 minutes at 45-50 °C, cooled to 40 °C, filtered and poured into water (300 mL). The aqueous layer was extracted with CH2Cl2 (3 x 200 mL) and the combined organic

layers were dried over Na2SO4. The solvent was removed by rotary evaporation to give a yellow liquid, which was purified by column chromatography (silica gel, CH2Cl2/hexane 1:4). 3.73 g

(13.4 mmol, 81 %) of the title compound was obtained as a white solid. Mp: 52-54 °C. 1H NMR (CDCl3, 300 MHz): 7.74 (dd, δ J = 7.7, J = 1.5, 2H), 7.14 (dd, J = 7.5, J = 1.8, 2H), 2.43 (s, 3H). 13C NMR (CDCl3, 75 MHz): 193.07, 138.29, 135.89, 127.69, 95.90,δ 30.20. IR (KBr, cm-1): 2962, 2922, 1907, 1695, 1466, 1382, 1354, 1260, 1122, 1005, 811.

1-Thioacetyl-4-[(trimethylsilyl)ethynyl]benzene (2.9)

This compound was prepared by a modification of the literature method.57

2.8 (1.34 g, 4.80 mmol) was dissolved in THF (7 mL).

Diisopropylethylamine (1.04 g, 8.04 mmol) and trimethylsilylacetylene (0.731 g, 7.44 mmol) were added and the mixture was stirred for 1 hour.

Dichlorobis(triphenylphosphine)palladium(II) (0.179 g, 0.26 mmol) and copper iodide (0.053 g 0.28 mmol) were added, all in the glovebox, and the reaction mixture was stirred 46 hours, after

which it was poured into water (30 mL). This mixture was extracted with ether (3 x 50 mL) and the combined organic layers were washed with a NH4Cl solution (2 x 75 mL) and brine (2 x 75

mL). The combined aqueous layers were extracted with ether (75 mL). All combined organic layers were dried over Na2SO4 and the solvent was removed by rotary evaporation to give 1.69 g

of a red oil. This crude product was purified by column chromatography twice (silica gel, hexane gradually increasing to hexane/CH2Cl2 4:1; then silica gel, hexane/CH2Cl2 1:1). 0.912 g (3.71

mmol, 77 %) of the title compound was obtained as a yellowish oil that crystallized upon standing.

Mp: 48-49 °C. 1H NMR (CDCl3, 300 MHz): 7.49 (dd, δ J = 7.5, J = 1.1, 2H), 7.34 (dd, J = 7.5, J = 1.5, 2H), 2.41 (s, 3H), 0.26 (s, 9H). 13C NMR (CDCl3, 75 MHz): 193.18, 134.00, 132.45,δ

128.29, 124.29, 104.13, 96.15, 30.18, -0.16. IR (KBr, cm-1): 2962, 2160, 1705, 1483, 1256, 1111, 869, 834.

61

Chapter 2

4-Ethynyl-1-thioacetylbenzene (2.10)

The conditions that were used for the preparation and the purification of this

compound were based on literature procedures.57,64 A solution of 2.9 (0.901 g, 3.63 mmol) in THF (16 mL) was cooled to 0 °C. A solution of TBAF (5.97 g,

18.9 mmol), acetic acid (0.92 mL, 16 mmol) and acetic anhydride (1.50 mL, 16 mmol) in THF (18 mL) was added dropwise, while keeping the temperature below 0 °C. The reaction mixture

was stirred for an additional 1.5 hours without cooling. Subsequently the mixture was filtered through a plug of silica and poured into water (50 mL). This mixture was extracted with CH 2Cl2

(4 x 20 mL) and the combined organic layers were washed with sat. NaHCO3 solution (3 x 40 mL), water (40 mL), and brine (40 mL). The combined aqueous layers were extracted with

CH2Cl2 (30 mL). All combined organic layers were washed one more time with brine (40 mL), dried over Na2SO4 and the solvent was removed by rotary evaporation to yield 0.617 g (3.50

mmol, 97 %) of the title compound as an orange-red oil. 1H NMR (CDCl3, 300 MHz): 7.51 (d, δ J = 8.1, 2H), 7.36 (d, J = 8.1, 2H), 3.16 (s, 1H), 2.41 (s,

3H). 13C NMR (CDCl3, 75 MHz): 193.10, 134.07, 132.59, 128.66, 123.21, 82.71, 78.85, 30.18.δ IR (NaCl, cm-1): 3286, 2960, 2927, 2104, 1708, 1483, 1397, 1353, 1124, 951, 829.

1-Bromo-4-tert-butylthiobenzene (2.11)

This compound was prepared by a literature method.40 A slurry of 4-bromothiophenol (99.18 g, 0.525 mol) in tert-butylchloride (400 mL) was stirred

for 30 minutes. Aluminium chloride (3.53 g, 26.5 mmol) was added in portions over one hour. The reaction mixture started to foam and HCl was formed. The reaction mixture

was stirred an additional hour and then poured into water (700 mL). The aqueous layer was extracted with pentane (3 x 150 mL). The combined organic layers were washed with water (2 x

100 mL), dried over Na2SO4 and the solvents were removed by rotary evaporation. Vacuum distillation (80 °C, 9 mTorr) afforded 109.3 g (0.446 mmol, 85%) of the title compound as a

colorless liquid. 1H NMR (CDCl3, 300 MHz): 7.46-7.36 (m, 4H), 1.27 (s, 9H). δ 13C NMR (CDCl3, 75 MHz): δ

138.85, 131.82, 131.58, 123.39, 46.02, 30.84. IR (NaCl, cm-1): 2961, 2940, 2922, 2896, 2861, 1468, 1363, 1168, 1092, 1071, 1011, 820.

1-tert-Butylthio-4-[(triisopropylsilyl)ethynyl]benzene (2.12)

This compound was prepared by a modification of literature methods.41 A mixture of 2.11 (7.40 g, 30.2 mmol), dichlorobis(triphenylphosphine)

palladium(II) (600 mg, 0.855 mmol) and copper iodide (396 mg, 2.08 mmol) was suspended in THF (210 mL). Diisopropylamine (30 mL) and

(triisopropylsilyl)acetylene (11.14 g, 61.1 mmol) were added and the reaction mixture was refluxed for 19 hours. The reaction mixture was poured into water (400 mL) and extracted with

diethylether (3 x 200 mL). The organic layers were washed with water (3 x 200 mL), dried over Na2SO4, filtered and the solvents were removed. Column chromatography (silica gel, heptane)

yielded 10.38 g (29.9 mmol, 99%) of the title compound as a yellowish liquid.1H NMR (CDCl3, 400MHz): 7.51-7.39 (m, 4H), 1.28 (s, 9H), 1.13 (s, 21H). δ 13C NMR (CDCl3,

62


100MHz): 137.09, 133.20, 131.91, 123.86, 106.45, 92.31, 46.39, 30.94, 18.65, 11.29. IR (cmδ -1):

2957, 2942, 2922, 2893, 2864, 2155, 1480, 1458, 1363, 1218, 1166, 1017, 996, 882, 832, 696, 673, 659. HRMS (APCI) calculated for [M+H]+ 347.22232, found 347.22342.

1-tert-Butylthio-4-ethynylbenzene (2.13)

This compound was prepared by a modification of literature methods.41 2.12 (10.0 g, 28.8 mmol) was dissolved in THF (100 mL) and cooled to 0 °C. A

solution of TBAF (18.5 g, 58.5 mmol) in THF (50 mL) was added dropwise over 30 minutes. The reaction mixture was stirred for 15 minutes at 0 °C and for 4 more hours

without cooling. The reaction mixture was filtered through a plug of silica gel, eluted with CH2Cl2, which yielded 17.7 g brown oil. This was purified by column chromatography (silica gel,

heptane/CH2Cl2 4:1) to yield 4.58 g (24.1 mmol, 84%) of the title compound as a yellowish liquid, that became a white solid in the fridge.1H NMR (CDCl3, 400MHz): 7.53-7.41 (m, 4H), 3.14 (s, 1H), 1.28 (s, 9H). δ 13C NMR (CDCl3, 100MHz): 137.12, 133.91, 131.99, 122.40, 83.07, 78.59, 46.43, 30.94. IR (cmδ -1): 3291, 2960,

2921, 2896, 2863, 2110, 1918, 1480, 1456, 1394, 1363, 1164, 1093, 1017, 833, 648, 638, 614. HRMS (APCI) calculated for [M+H]+ 191.08890, found 191.08879.

2.8.4 Synthesis and Analysis of the Anthraquinone and Anthracene Precursors (2.14-2.18)

2,6-Dibromo-9,10-anthraquinone (2.14)

This compound was prepared by literature methods.35,36 A mixture of anhydrous copper(II)bromide (28.0 g, 125 mmol), tert-butyl nitrite (17.2 mL,

145 mmol) and acetonitrile (200 mL) was heated to 60 °C and 2,6-diamino-9,10-anthraquinone (11.60 g, 48.7 mmol) was added in portions over 10

minutes. The reaction mixture stirred for 2 hours at 57 °C and for 1.5 hours at 70 °C, cooled and poured into 18% HCl solution (1 L). The brown precipitate was filtered, washed with water (10 x

200 mL) and acetonitrile (10 x 200 mL), and dried in the vacuum oven. The crude product was recrystallized from bromobenzene (1 L) with hot filtration to give 11.34 g (31.0 mmol, 64%) of

the title compound as a dark yellow crystals.Mp: 276-281 °C. 1H NMR (300 MHz, CDCl3) 8.44 (d, δ J = 2.0, 2H), 8.17 (d, J = 8.3, 2H), 7.95

(dd, J = 8.3, 2.0, 2H). 13C NMR (C2D2Cl4, 125 MHz, 80 °C): 179.66, 135.89, 132.97, 130.41,δ 128.83, 128.68, 127.60. IR (KBr, cm-1): 3086, 3065, 1673, 1574, 1309, 1286, 1163, 1106, 1069,

956, 914, 858, 816, 732, 711, 666.

2,6-Dibromo-9,10-diacetoxyanthracene (2.15)

This compound was prepared by a literature procedure.35 Acetic anhydride

(75 mL) was added to 2.14 (1.84 g, 5.03 mmol), zinc dust (1.79 g, 27 mmol, activated by stirring for 1 hour in 10% HCl solution, and then filtering and

washing with water and acetone) and anhydrous sodium acetate (0.65 g, 7.9 mmol) and the reaction mixture was stirred for 80 minutes. Then the reaction mixture was

63

Chapter 2

refluxed for 90 minutes and cooled to room temperature. Water (60 mL) was added and the

mixture was refluxed again for 10 minutes. After cooling, the yellow precipitate was filtered off and washed with water (6 x 120 mL). The crude product was dried in the vacuum oven to give

2.28 g of a yellow powder. This was dissolved in CH2Cl2 (600 mL) and filtered to remove traces of zinc powder. The CH2Cl2 was removed by rotary evaporation and 1.84 g (4.07 mmol, 81 %) of

the title compound was obtained as a yellow solid. Mp: 298-301 °C. 1H NMR (CDCl3, 300 MHz): 8.08 (d, δ J = 1.8, 2H), 7.79 (d, J = 9.2, 2H), 7.58

(dd, J = 9.3, J = 1.6, 2H), 2.65 (s, 6H). 13C NMR (C2D2Cl4, 100 MHz): 168.04, 138.27, 129.37,δ 123.52, 122.41, 122.26, 121.63, 120.32, 19.49. IR (KBr, cm -1): 3072, 3027, 2935, 1755, 1611,

1446, 1429, 1365, 1356, 1200, 1164, 1069, 1049, 896, 860, 801, 754.

2,6-Dibromo-9,10-dimethoxyanthracene (2.16)

This compound was prepared by a modification of the literature methods.36

2.14 (2.00 g, 5.48 mmol), tetrabutylammonium bromide (1.68 g, 5.21 mmol), and sodium dithionite (2.18 g, 14.8 mmol) were suspended in water (50 mL,

purged with N2). CH2Cl2 (60 mL, purged with N2) was added and the dark green emulsion was stirred for 2.5 hours. Then 20% NaOH was added (50

mL, 257 mmol) and the reaction mixture turned magenta, after which it was stirred for another 2.5 hours. Iodomethane (53 mL, 858 mmol) was added and the reaction mixture was stirred for

20 hours, and poured into water (250 mL). The mixture was extracted with CH 2Cl2 (3 x 100 mL) and the organic layers were washed with water (5 x 200 mL), dried over Na 2SO4, filtered, and

concentrated. The resulting 2.3 g orange solid was preadsorbed onto silica and purified by column chromatography (silica gel, heptane/CH2Cl2 2:1), to afford 561 mg (1.42 mmol, 24%) of

the title compound as a yellow solid.1H NMR (400 MHz, CDCl3): 8.43 (d, δ J = 1.5, 2H), 8.15 (d, J = 9.2, 2H), 7.55 (dd, J = 9.2, 1.9,

2H), 4.09 (s, 6H). 13C NMR (125 MHz, CDCl3): 147.89, 129.51, 125.80, 124.65, 124.53,δ 123.80, 120.46, 63.64. IR (cm-1): 3086, 3004, 2964, 2936, 2842, 1604, 1449, 1435, 1348, 1071,

1051, 964, 880, 813, 793, 711. HRMS (APCI) calculated for [M+H]+ 396.92563, found 396.92652. Calcd for C16H12Br2O2: C, 48.52; H, 3.05. Found: C, 48.26; H, 2.93.

2,6-Dibromoanthracene (2.17)

This compound was prepared by a modification of literature methods.45,46

2.14 (3.23 g, 8.83 mmol) was suspended in a mixture of methanol (50 mL)

and toluene (40 mL) and cooled to 0 °C. NaBH4 (10.7 g, 283 mmol) was added in portions over 2.5 hours. Toluene (15 mL) and methanol (15 mL) were added and the

reaction mixture was stirred for 16 hours and subsequently refluxed for 2.5 hours. After cooling to room temperature the reaction mixture was poured into N2 purged ice water (600mL), filtered

and washed with water (500 mL). The obtained solid was stirred for 17 hours in 5 M HCl (100 mL), filtered, washed with water (500 mL), and dried. The dried solid was suspended in

isopropanol (30 mL) and NaBH4 (8.31 g, 220 mmol) was added. The reaction mixture was refluxed for 70 hours, poured into N2 purged ice water (400 mL), filtered and washed with water

(500 mL) and dried. Recrystallization from toluene afforded 543 mg (1.62 mmol, 18%) of the title compound as yellow crystals.1H NMR (400 MHz, CDCl3): 8.30 (s, 2H), 8.17 (d, δ J = 2.0, 2H), 7.87 (d, J = 9.0, 2H), 7.53 (dd,

64


J = 9.0, 2.0, 2H). 13C NMR (CDCl3, 125 MHz): δ 132.41, 130.26, 129.90, 129.79, 129.59,

125.69, 119.90. IR (cm-1): 3065, 1924, 1803, 1727, 1607, 1526, 1442, 1334, 1283, 1153, 1047, 963, 912, 898, 868, 793, 746, 709, 626.

2,6-Dibromo-9,10-dihydroanthacene (2.18)

2.14 (5.27 g, 14.4 mmol), red phosphorus (4.20 g, 136 mmol) and iodine (1.00 g, 4.0 mmol) were placed in an ampule and HI (50 mL, 57% w/w in

water) was added. The ampule was sealed and heated to 130-142 ºC for 3 days. After cooling an opening of the ampule, the suspension was poured into water (400 mL)

and filtered. The residue was washed with cold water (200 mL) and hot water (200 mL) and dried on air. The resulting solid was dissolved in CH2Cl2 (400 mL), dried over Na2SO4, filtered,

and all volatiles were removed to afford 4.1 g white solid. This was recrystallized from ethanol to yield 2.81 g (8.31 mmol, 58%) of the title compound as white needles.1H NMR (500 MHz, CDCl3): 7.43 (d, δ J = 1.9, 2H), 7.32 (dd, J = 8.0, 2.0, 2H), 7.14 (d, J = 8.0, 2H), 3.85 (s, 4H). 13C NMR (125 MHz, CDCl3): 138.35, 134.77, 130.28, 129.25, 128.96,δ

119.89, 35.28. IR (cm-1): 3082, 3052, 3024, 2933, 2853, 2806, 1593, 1474, 1414, 1391, 1173, 1129, 1076, 957, 913, 885, 871, 802, 724. Calcd for C14H14Br2: C, 49.74; H, 2.98. Found: C,

48.74; H, 2.82.

65

Chapter 2

2.9 References and Notes1. E.H. van Dijk, D.J.T. Myles, M.H. van der Veen, J.C. Hummelen, Org. Lett. 2006, 8, 2333-

2336.

2. S.J. van der Molen, P. Liljeroth, J. Phys.: Condens. Matter 2010, 22, 133001.

3. M. Irie, Chem. Rev. 2000, 100, 1685-1716.

4. N. Katsonis, M. Lubomska, M.M. Pollard, B.L. Feringa, P. Rudolf, Prog. Surf. Sci. 2007, 82, 407-434.

5. D. Dulić, S.J. van der Molen, T. Kudernac, H.T. Jonkman, J.J.D. de Jong, T.N. Bowden, J. van Esch, B.L. Feringa, B.J. van Wees, Phys. Rev. Lett. 2003, 91, 207402.

6. S.J. van der Molen, H. van der Vegte, T. Kudernac, I. Amin, B.L. Feringa, B.J. van Wees, Nanotechnology 2006, 17, 310-314.

7. T. Kudernac, S.J. van der Molen, B.J. van Wees, B.L. Feringa, Chem. Commun. 2006, 3597-3599.

8. J. He, F. Chen, P.A. Liddell, J. Andréasson, S.D. Straight, D. Gust, T.A. Moore, A.L. Moore, J. Li, O.F. Sankey, S.M. Lindsay, Nanotechnology 2005, 16, 695-702.

9. N. Katsonis, T. Kudernac, M. Walko, S.J. van der Molen, B.J. van Wees, B.L. Feringa, Adv. Mater. 2006, 18, 1397-1400.

10. A.J. Kronemeijer, H.B. Akkerman, T. Kudernac, B.J. Wees, B.L. Feringa, P.W.M. Blom, B. de Boer, Adv. Mater. 2008, 20, 1467-1473.


12. J. Areephong, W.R. Browne, N. Katsonis, B.L. Feringa, Chem. Commun. 2006, 3930.

13. B.Q. Xu, X.L. Li, X.Y. Xiao, H. Sakaguchi, N.J. Tao, Nano Lett. 2005, 5, 1491-1495.

14. I.V. Pobelov, Z. Li, T. Wandlowski, J. Am. Chem. Soc. 2008, 130, 16045-16054.

15. E. Wang, H. Li, W. Hu, D. Zhu, J. Polym. Sci., Part A: Polym. Chem. 2006, 44, 2707-2713.

16. E.J. Wang, C.L. Wang, Q. Meng, H.X. Li, W.P. Hu, D.B. Zhu, Chin. Chem. Lett. 2008, 19, 1285-1289.

17. F. Giacalone, M.A. Herranz, L. Grüter, M.T. González, M. Calame, C. Schönenberger, C.R. Arroyo, G. Rubio-Bollinger, M. Vélez, N. Agraït, N. Martín, Chem. Commun. 2007, 4854-4856.

18. J. Liao, J.S. Agustsson, S. Wu, C. Schonenberger, M. Calame, Y. Leroux, M. Mayor, O. Jeannin, Y. Ran, S. Liu, S. Decurtins, Nano Lett. 2010, 10, 759-764.

19. N. Weibel, A. Blaszczyk, C. von Hänisch, M. Mayor, I. Pobelov, T. Wandlowski, F. Chen, N. Tao, Eur. J. Org. Chem. 2008, 136-149.

20. C. Wang, M.R. Bryce, J. Gigon, G.J. Ashwell, I. Grace, C.J. Lambert, J. Org. Chem. 2008, 73, 4810-4818.

21. J.K. Sørensen, M. Vestergaard, A. Kadziola, K. Kilså, M.B. Nielsen, Org. Lett. 2006, 8, 1173-1176.

22. M. Vestergaard, K. Jennum, J.K. Sørensen, K. Kilså, M.B. Nielsen, J. Org. Chem. 2008, 73, 3175-3183.

66

23. G. Chen, Y. Zhao, Tetrahedron Lett. 2006, 47, 5069-5073.

24. Conductance measurements in gated electromigration junctions have been performed recently on a molecule from the family in Figure 2.3a by Jeppe Fock in the group of prof. Herre van der Zant at University of Delft (poster communication at the ElecMol'10 conference, 6-10 December 2010, Grenoble).

25. F.F. Fan, J. Yang, S.M. Dirk, D.W. Price, D. Kosynkin, J.M. Tour, A.J. Bard, J. Am. Chem. Soc. 2001, 123, 2454-2455.

26. F.F. Fan, J. Yang, L. Cai, D.W. Price, S.M. Dirk, D.V. Kosynkin, Y. Yao, A.M. Rawlett, J.M. Tour, A.J. Bard, J. Am. Chem. Soc. 2002, 124, 5550-5560.

27. S.A. Trammell, D.S. Seferos, M. Moore, D.A. Lowy, G.C. Bazan, J.G. Kushmerick, N. Lebedev, Langmuir 2007, 23, 942-948.

28. S. Tsoi, I. Griva, S.A. Trammell, A.S. Blum, J.M. Schnur, N. Lebedev, ACS Nano 2008, 2, 1289-1295.

29. D. J. T. Myles, M. H. van der Veen, E. H. van Dijk, J. C. Hummelen, unpublished results.

30. The protonated acridone wire was analyzed by 1H NMR spectroscopy (in DMSO-d6) and IR. Washing of a suspension of this protonated acridone in chloroform with water yielded the acridone-wire back.

31. J. L. H. Otten, Bachelor Thesis "An anthracene-based molecular wire: synthesis and switching behaviour", University of Groningen, 2008.

32. K. Sonogashira, Y. Tohda, N. Hagihara, Tetrahedron Lett. 1975, 4467-4470.

33. R. Chinchilla, C. Nájera, Chem. Rev. 2007, 107, 874-944.

34. Addition of the amine to the reaction mixture in general turned the yellow suspension into an orange-red solution, before the acetylene was added. This observation indicates that Pd(II) is reduced to Pd(0) by the amine.

35. J. Yang, A. Dass, A.M. Rawashdeh, C. Sotiriou-Leventis, M.J. Panzner, D.S. Tyson, J.D. Kinder, N. Leventis, Chem. Mater. 2004, 16, 3457-3468.

36. S.K. Lee, W.J. Yang, J.J. Choi, C.H. Kim, S. Jeon, B.R. Cho, Org. Lett. 2005, 7, 323-326.

37. D.T. Gryko, C. Clausen, K.M. Roth, N. Dontha, D.F. Bocian, W.G. Kuhr, J.S. Lindsey, J. Org. Chem. 2000, 65, 7345-7355.

38. D.L. Pearson, J.M. Tour, J. Org. Chem. 1997, 62, 1376-1387.

39. M. Mayor, H.B. Weber, J. Reichert, M. Elbing, C. von Hänisch, D. Beckmann, M. Fischer, Angew. Chem., Int. Ed. 2003, 42, 5834-5838.

40. N. Stuhr-Hansen, Synth. Commun. 2003, 33, 641-646.

41. A. Blaszczyk, M. Elbing, M. Mayor, Org. Biomol. Chem. 2004, 2, 2722-2724.

42. No pure 2.4A could be obtained from a direct Sonogashira cross-coupling between 2.15 and 2.10.

43. See for the synthesis of the asymmetric analogue of 2.5B (with one thiol terminal only): E. H. van Dijk, MSc Thesis “An Anthraquinone-Based Switch for Molecular π-Logic”, University of Groningen, 2006.

44. M.F. Semmelhack, T. Neu, F. Foubelo, J. Org. Chem. 1994, 59, 5038-5047.

45. T.R. Criswell, B.H. Klanderman, J. Org. Chem. 1974, 39, 770-774.

67

Anthraquinone- and Anthracene-based

Molecular

Wires

and

Switches

46. P. Hodge, G.A. Power, M.A. Rabjohns, Chem. Commun. 1997, 73-74.

47. N. Stuhr-Hansen, J.K. Sørensen, K. Moth-Poulsen, J.B. Christensen, T. Bjørnholm, M.B. Nielsen, Tetrahedron 2005, 61, 12288-12295.

48. R.N. Renaud, J.C. Stephens, Can. J. Chem. 1974, 52, 1229-1230.

49. F. Keller, C. Rüchardt, J. Prakt. Chem./Chem.-Ztg. 1998, 340, 642-648.

50. F. Ilhan, D.S. Tyson, D.J. Stasko, K. Kirschbaum, M.A. Meador, J. Am. Chem. Soc. 2006, 128, 702-703.

51. S.-K. Kwon et al., patent WO 2008/120839, October 9, 2008

52. R. K. Bailey et al., patent WO 2008/010983, January 24, 2008

53. For proposed mechanisms on the discussed reductions, see D. Albouy, G. Etemad-Moghadam, M. Vinatoru, M. Koenig, J. Organomet. Chem. 1997, 529, 295-299; D. Albouy, G. Etemad-Moghadam, M. Koenig, Eur. J. Org. Chem. 1999, 1999, 861-868; L.D. Hicks, J.K. Han, A.J. Fry, Tetrahedron Lett. 2000, 41, 7817-7820.

54. Partial charge transfer could take place from the electron rich thio-functionalized phenylacetylene units to the electron poor anthraquinone unit.

55. N.N.P. Moonen, W.C. Pomerantz, R. Gist, C. Boudon, J. Gisselbrecht, T. Kawai, A. Kishioka, M. Gross, M. Irie, F. Diederich, Chem. Eur. J. 2005, 11, 3325-3341.


57. Time resolved photoluminescence measurements were performed by Jia Gao and Jochem Smit, University of Groningen.

58. A. Babaei, P.A. Connor, A.J. McQuillan, S. Umapathy, J. Chem. Educ. 1997, 74, 1200-1204.

59. N.G. Connelly, W.E. Geiger, Chem. Rev. 1996, 96, 877-910.

60. K. Kuwata, D.H. Geske, J. Am. Chem. Soc. 1964, 86, 2101-2105.

61. N. Wiberg, Angew. Chem. 1968, 80, 809-822.

62. S.M. Lindner, N. Kaufmann, M. Thelakkat, Org. Electron. 2007, 8, 69-75.

63. S.C. Veenstra, U. Stalmach, V.V. Krasnikov, G. Hadziioannou, H.T. Jonkman, A. Heeres, G.A. Sawatzky, Appl. Phys. Lett. 2000, 76, 2253.

64. M. Nielsen, K. V. Gothelf, J. Chem. Soc., Perkin Trans. 1 2001, 19, 2440.

68

Chapter 2

Chapter 3Controlling the Formation of Self-Assembled Monolayers of Conjugated Thiols on Gold

In this chapter we report a systematic study on the formation of self-assembled monolayers (SAMs) of conjugated molecules for molecular electronic (ME) devices. We monitored the deprotection reaction of acetyl protected dithiols of oligo(phenylene ethynylenes) (OPEs) in solution using two different bases and studied the quality of the resulting SAMs on gold. We found that the optimal conditions to reproducibly form dense, high-quality monolayers are 9-15% triethylamine (Et3N) in THF. The deprotection base tetrabutylammonium hydroxide (Bu4NOH) leads to less dense SAMs and incorporation of Bu4N+ ions into the monolayer. Furthermore, our results show the importance of the equilibrium concentrations of (di)thiolate in solution on the quality of the SAM. To demonstrate the relevance of these results for molecular electronics applications, large-area molecular junctions were fabricated using no base, Et3N, and Bu4NOH. The magnitude of the current densities in these devices is highly dependent on the base. The current density of SAMs of OPEs of increasing length formed using Et3N was found to decay exponentially with β = 0.15 Å-1.

69

Chapter 3

3.1 IntroductionIn Chapter 1 we have introduced our Matrix Approach for which we need to

contact our conjugated molecular wires to different types of electrodes, to measure

and compare the conductances within the different series. We have chosen to use

the self-assembly of thiols on gold as the main tool to establish these contacts to

our molecules. However, we have synthesized our molecules with acetyl-protected

thiols. Our first attempts to grow monolayers either directly from this

dithioacetates or after deprotecting with aqueous ammonia1 resulted in low

coverages or multilayers, which obfuscated electronic measurements in Large Area

Molecular Junctions (LAMJs, see Section 1.4.5).2 For this reason, we investigated

in situ deprotection of our dithioacetates by different bases and its influence on the

quality and density of self-assembled monolayers (SAMs) of our oligo(phenylene

ethynylenes) (OPEs) in detail and found striking differences, that we have

summarized in Figure 3.1. In Section 3.6 we will demonstrate the high-quality of

our SAMs in LAMJs and describe the length dependence of the charge transport

through OPEs.

3.1.1 Why Studying the Formation of Self-Assembled Monolayers?

Conjugated molecules and, in particular OPEs and phenylenes, are a critical

component of ME devices3,4 because they enable the control of the tunneling of

electrons by synthetic chemistry. In these devices the SAM is used to define the

smallest dimension of the device (i.e., the tunnel-junction between the electrodes),

70

Figure 3.1 A schematic of the self-assembled monolayers on gold that are formed from solutions of OPE and terphenyl dithioesters in THF: without base a SAM of about 70% of the maximum density is formed, with 9-15 % (v/v) Et3N densely-packed SAMs are formed, and with 4 equivalents of Bu4NOH the molecules lay flat on the surface and Bu4N+ is incorporated in the SAM.

Controlling the Formation of Self-Assembled Monolayers of Conjugated Thiols on Gold

while the lateral dimension can be relatively large (up to hundreds of microns).

Therefore the reliable, reproducible formation of densely-packed,5 high-quality6

SAMs over large areas is absolutely required. This is in contrast to the formation of

junctions of single molecules—e.g., mechanically-controllable break junctions and

STM break junctions—where lower coverages are often preferred over densely-

packed SAMs. These issues are less evident for SAMs of alkanethiolates because

of the well-known insensitivity of the quality of these SAMs to the conditions of

formation.7 However, unlike simple alkanes, conjugated molecules are not

sufficiently air-stable as free thiols to form SAMs and therefore must be protected,

typically as acetyl thioesters, because they are stable and easy to prepare. Thus,

SAMs are routinely formed by cleaving the acetyl thioesters with a base, generating

the free thiolate in situ. The exact procedure —base, concentrations of thioester

and base, immersion times, etc.— of this deprotection, however, varies somewhat

arbitrarily between laboratories and studies. This lack of reproducible protocols

and adequate characterization hinders the meaningful interpretation of electronic

measurements on devices containing these conjugated SAMs.

The first study on the formation of SAMs from conjugated thiols, acetyl thioesters,

and deprotected thioacetates was reported by Tour et al.1 They demonstrated that

the ellipsometric thicknesses of SAMs of conjugated monothiols grown from THF

reach the expected value within 24 h, while dithiols form multilayers.1,8 If the

dithiols are first protected as acetyl thioesters, the resulting SAMs do not form

multilayers, but are thinner than expected1 (in agreement with other studies9 and

with our results, although Lau et al. disagree10). When the acetyl thioesters are

removed in situ with NH4OH, Tour et al. also observe the formation of multilayers.1

Despite this observation, over the past 15 years this paper has been frequently and

incorrectly cited as evidence of the formation of high-quality SAMs of conjugated

dithiols formed from the in situ deprotection of acetyl thioesters with NH4OH.

Some studies report reasonable thicknesses using NH4OH,111213

-14

15 others report

thicknesses that are higher than the calculated value,9,16,17 and impurities attributed

to the NH4OH are reported.18 The problem with NH4OH is that it is only effective

in polar, protic solvents (usually ethanol, which is also commonly used with

alkanethiols). Conjugated, rigid-rod molecules such as OPEs and phenylenes,

however, are not compatible with protic solvents, thus SAMs of these molecules

are typically formed from aprotic solvents (usually THF). This incompatibility

makes it impossible to control the concentration of NH4OH (which is 30%

aqueous NH3) because it is lost as NH3, particularly while sparging with an inert

71

Chapter 3

gas. Despite this fact, NH4OH is commonly used in aprotic solvents, which can

lead to irreproducible, low-quality, loosely-packed SAMs. Using NaOH as

deprotecting agent causes similar problems19 and damages the metal substrate.20

Tour et al. used Et3N to favor the thiolate form of thiophenethiol over the dimeric

form,1, 21 but not to deprotect thioesters. Other studies use Et3N to form thiols from

non-thioester precursors.22,23 Shaporenko et al. compared SAMs formed from

biphenyldiacetylthiolate using "appropriate amounts" of Et3N to those using

NH4OH and found that the former produced SAMs that were more densely-

packed.16 There are other studies on the deprotection of conjugated OPE

monothioacetates,2425

-26 however they focus on other aspects (e.g., reactions between

the deprotecting agent and other functional groups) and do not observe the

difficulties that are inherent to dithiols. We chose to study Bu4NOH as a non-

volatile analog of NH4OH because it is commonly used to deprotect conjugated

dithioacetates in situ for ME measurements in mechanically-controllable break-

junctions27 and STM break-junctions.28 We chose Et3N because of the promising

results of Shaporenko et al., and the need for high-quality, densely-packed SAMs

of conjugated molecules for ME devices using, for example, µ-contact printing,2930

-31

conjugated polymers,2,32 Hg,33,34 eutectic GaIn,35 and CP-AFM3637

-38 to contact the

SAM (see Chapter 1.4).39,40

3.2 Synthesis of Oligo(phenylene ethynylene)sWe synthesized the OPEs according to the strategy that was described in Chapter

2. The core of the OPE is made by Sonogashira cross-coupling reactions. As in the

previous chapter, we choose to use tert-butyl protected thiols in the cross-couplings,

that are in the last step converted into acetyl protected thiol upon treatment with

boron tribromide and acetyl chloride.

We use the number of phenyl rings as a suffix to name the OPE molecules of

different length, thus OPE3 is a para oligo(phenylene ethynylene) with three

phenyl rings (and two acetylenes to connect the three phenyl rings). We use the

prefix "StBu" for tert-butyl protected thiols and the prefix "SAc" for acetyl protected

thiols. Prefixes "diStBu" and "diSAc" are used for bis tert-butyl protected and bis

acetyl protected dithiols respectively. Thiolates are abbreviated as "S" (i.e., we omit

the minus sign of S–).

72


3.2.1 Oligo(phenylene ethynylene) dithioacetates

Stuhr-Hansen et al. have described the synthesis of diSAc-OPE341 according to this

strategy.42 We have conveniently followed their protocols, on a larger scale and

obtained diStBu-OPE3 and diSAc-OPE3 both in 74% yield (Scheme 3.1). We

synthesized diStBu-OPE2 by coupling bromide 2.11 with acetylene 2.13 (see

Chapter 2) in 60% yield and converted this into diAc-OPE2 43 in 91%. DiStBu-

OPE4 was synthesized by a cross-coupling of bis-bromide 3.1, that was

synthesized in one step as described in the literature,44 and acetylene 2.13 in 50%.

DiStBu-OPE4 was then converted into diSAc-OPE4 upon 4 days reaction with

boron tribromide and acetyl chloride in 43% yield. This long reaction time was

required due to the low solubility of both diStBu- and diSAc-OPE4. The low

solubility of diSAc-OPE4 hindered purification by column chromatography, but

allowed recrystallization.

3.2.2 Asymmetric Oligo(phenylene ethynylene) thioacetates

We have synthesized SAc-OPE2 and SAc-OPE3, but not SAc-OPE4 because the

expected solubility of SAc-OPE4 is lower than that of diSAc-OPE4 and most

likely too low for the formation of a self-assembled monolayer.45 The Sonogashira

cross-coupling of bromide 2.11 with phenyl acetylene yielded StBu-OPE2 in 74%,

which was conveniently converted into SAc-OPE2 in 84% yield. For the synthesis

of asymmetric StBu-OPE3 we used the difference in reactivity between a bromide

and iodide in Sonogashira cross-couplings: the iodide of 1-bromo-4-iodobenzene

73

Scheme 3.1 Syntheses of diSAc-OPE2-4: (i) Pd(PPh3)2Cl2, CuI, iPr2NH, THF, reflux; (ii) Pd(PPh3)2Cl2, CuI, Et3N, THF, toluene; (iii) BBr3, AcCl, CHCl3, toluene.

Chapter 3

reacts at room temperature, whereas the bromide requires elevated temperatures.

We first coupled 1-bromo-4-iodobenzene with acetylene 2.13 to obtain 3.2 in 50%

yield. A subsequent cross-coupling with phenyl acetylene yielded StBu-OPE3 in

80%. The reaction with boron tribromide and acetyl chloride then yielded SAc-

OPE3 in 88%.

3.3 Deprotection of Acetyl Protected Thiols and the Formation of SAMs on GoldThe formation of SAMs of alkanethiols has been described in detail. 46 However,

less is known on the formation of SAMs from conjugated thiols, 47 and to the best

of our knowledge, no description is given for the formation of SAMs from

deprotected thioacetates. For that reason, we will first introduce the concepts that

are involved in this process in Section 2.3.1 and Figure 3.2 and then present the

data that support this hypothesis in the following sections.

74

Scheme 3.2 Syntheses of SAc-OPE2 and SAc-OPE3: (i) Pd(PPh3)2Cl2, CuI, iPr2NH, THF, reflux; (ii) Pd(PPh3)2Cl2, CuI, Et3N, THF; (iii) phenyl acetylene, Pd(PPh3)2Cl2, CuI, iPr2NH, THF, reflux; (iv) BBr3, AcCl, CHCl3, toluene.


3.3.1 Formation of SAMs from Conjugated Dithioesters.

The deprotection of thioacetates by a base yields thiolate anions, which can bind

to gold very easily to form a self-assembled monolayer (SAM). The formation of a

75

Figure 3.2 A schematic of the kinetics of the formation of SAMs on gold from solutions of a. diSAc only: incomplete coverage due to weak association with the surface and slow incorporation into the monolayer. b. diS only: strong association with the gold surface hinders self-assembly; polymeric disulfides form readily and precipitate. c. diSAc plus SAcS: self-assembly occurs similarly to diSAc-only except SAcS incorporates readily, resulting in a densely-packed monolayer.

Chapter 3

SAM in general occurs in three basic steps: i) association between molecules and

substrate where the molecules lie down on the surface, ii) reorganization of these

molecules into islands of loosely-packed standing molecules (observed as striped

phases for alkanethiolates), and iii) growth of these islands into a densely-packed

monolayer.46 The transition from lying-down to standing up is driven by the

strength of the Au-thiolate bond and can only occur if the association with surface

is weak enough to be reversible on the timescale of the experiment (dotted lines in

Figure 3.2a). Likewise, the growth of the domains of standing molecules can only

occur if each step is reversible and the densely-packed monolayer is the most

thermodynamically stable situation. Thiolates associate much more strongly than

thiols or thioesters, but Au cleaves thioesters (and thiols) to form Au-thiolates. The

resulting Au-bound thiolates dissociate as Au complexes, thus they do not

participate in deprotection reactions or the formation of SAMs.

SAMs of diS-OPE (Figure 3.2b) are arrested at step i: interactions between the Au

surface and the π-electrons in combination with two highly reactive thiolates drives

the equilibrium between the standing-up phase and lying-down too far toward the

lying-down phase for a SAM to form. By contrast, in a solution comprising mainly

diSAc-OPE3 and/or SAc-OPE3-S, the equilibrium is pushed towards the standing-

up phase by the poor interaction of the SAc groups with the Au surface, combined

with the favorable packing of the molecules in the SAM. Though diSAc-OPE

tends to form standing-up SAMs (Figure 3.2a), the thioacetates are too bulky to fill

the last vacancies in the SAM. This can be solved by the presence of SAc-OPE-S in

the solution (Figure 3.2c), even in small quantities.

In Figure 3.2 we have not drawn the situation for a SAM to grow from only SAc-

OPE-S, which would be the ideal species, with one strong binding and fast reacting

thiolate and one weak binding, protected thiol.48 We have not included this, since it

is impossible to have a solution of pure SAc-OPE-S, due to thioester metathesis

(see Scheme 3.3): a mixture of thioesters, in the presence of a thiolate (i.e., R-S, not

R-SH), will metathesize to form equilibrium mixtures that reflect the initial

76

Scheme 3.3 Mechanism for the thioester metathesis.


concentration of thiolate and the relative stabilities of the various thiolates and

thioesters.49,50 For example, introducing R2-S to a solution of R1-SAc forms a

mixture of R1-SAc, R1-S, R2-SAc, and R2-S. Since this equilibration occurs on a µs

timescale in solution and the formation of a SAM occurs at the interface between

the solution and the substrate on a minute timescale, the solution from which the

SAM forms is highly dependent on how much thiolate is generated from the

deprotecting agent. (The removal of thiolate by the growing SAM has a negligible

impact at the concentrations typically used.) This means that, in the case of

deprotecting a dithioacetate, there will be a competition between the diSAc-OPE,

SAc-OPE-S, and diS-OPE.

3.3.2 Deprotection by Tetrabutylammonium Hydroxide

We followed the deprotection reaction of acetyl-protected thiols with

tetrabutylammonium hydroxide (Bu4NOH) by recording UV-Vis spectra of 0.3

mM diSAc-OPE3 in THF during the addition of six equivalents (relative to the

77

Figure 3.3 UV-Vis absorption spectra of 0.3 mM solutions of diSAc-OPE3, SAc-OPE3, diSAc-OPE2, and SAc-OPE2 in THF, with 0 (black), 1 (blue), 2 (green), 3 (orange), 4 (red), and 6 (dark red) eq. of Bu4NOH, showing the conversion of thioacetate into free thiolate.

Chapter 3

number of diSAc-molecules; i.e., three eq. per SAc) of Bu4NOH. The solutions

changed from colorless to bright orange to yellow as the free thiolates formed

(Figure 3.3, top left). During the addition of the first two eq. of Bu4NOH, a new

absorption peak appeared at 460 nm which we ascribe to delocalized thiolates.

This peak increased in intensity and gradually shifted to 458 nm during the

addition of eq. three and four and remained constant through eq. five and six,

indicating that two eq. of Bu4NOH react with each SAc in diSAc-OPE3. We

repeated this experiment with SAc-OPE3, SAc-OPE2, and diSAc-OPE2 and

observed the same result: two eq. of Bu4NOH remove one Ac.

The first eq. hydrolyzes the Ac through simple addition/elimination and the

second deprotonates the acetic acid that is formed in the first step (Scheme 3.4).

The linear dependence of the increase in intensity at 458 nm and commensurate

decrease at 331 nm on the amount of Bu4NOH, and the semi-isosbestic point at

363 nm suggest that there are no intermediate chromophores between the diSAc-

OPE3 and diS-OPE3 compounds. There must, however, be a mono-deprotected

intermediate (SAc-OPE3-S). This is more clear from the UV-Vis spectra of diSAc-

OPE2 with up to six eq. Bu4NOH. The spectrum measured after addition of two

eq. is clearly not a combination of the spectrum of diSAc-OPE2 (zero eq.) and that

of diS-OPE2 (four eq.), indicating the presence of intermediate SAc-OPE2-S.51

To probe for the SAc-OPE3-S intermediate we prepared four solutions of 0.3 mM

diSAc-OPE3 in THF-d8 with zero eq., half an eq., two eq., and four eq. of

Bu4NOH and examined them using 1H NMR spectroscopy. The spectrum of the

solution containing four eq. of Bu4NOH consisted of three peaks (Figure 3.4c) that

are shifted up-field relative to diSAc-OPE3 (Figure 3.4a) which we ascribe to diS-

OPE3 (see also Figure 3.6) Assuming that the solution containing two eq. of

Bu4NOH (Figure 3.4b) comprised a mixture of diSAc-OPE3, SAc-OPE3-S, and

diS-OPE3, we subtracted these two spectra (a and c) from (b) to isolate the

spectrum of SAc-OPE3-S (Figure 3.4d). We integrated the peaks in the aromatic

region (6.7-7.7 ppm) to determine that the solution with two eq. Bu4NOH

78

Scheme 3.4 Mechanism for the reaction of a thioacetate with 2 equivalents of hydroxide.


comprised 22% diSAc-OPE3, 56% SAc-OPE3-S, and 22% diS-OPE3—a ratio of

1:2:1. We repeated this analysis and determined that ratio of the solution

containing half an eq. of Bu4NOH was 3:1:0.52 This means that the three species

coexist as a statistical mixture in solution (due to the metathesis of the thioesters),

in a ratio determined by the amount of Bu4NOH and with no preference for the

formation of a particular species. These observations are in agreement with the

UV-Vis data, which show a single absorption growing in intensity with the

addition of Bu4NOH, meaning that the absorptions of the thiolates of SAc-OPE3-

S and diS-OPE3 are nearly identical.51

79

Figure 3.4 1H NMR spectra from 7.7-6.7 ppm, of 0.3 mM diSAc-OPE3 in THF-d8 (a), with addition of 2 eq. Bu4NOH (b), with addition of 4 eq. Bu4NOH (c), and the spectrum of b with a and c subtracted (d), which shows that in addition to diSAc-OPE3 and diS-OPE3, the asymmetric SAc-OPE3-S persists in the solution with 2 eq. Bu4NOH.

Chapter 3

We examined the influence of the concentration of Bu4NOH on the formation of

SAMs of OPEs by immersing Au substrates in 0.3 mM solutions of diSAc-OPE3

and either zero, one, two, or four eq. of Bu4NOH and measuring the thicknesses

of the resulting SAMs using ellipsometry (Figure 3.5a). These values are based on

the assumptions that the index of refraction of a monolayer of conjugated

molecules is 1.55,1,11 and that the absorption of the SAMs can be neglected; they

are accurate to ±2 Å. Lower values indicate a SAM that is less densely-packed,5

but we cannot determine the cause (i.e., the structure of the SAM) using only

ellipsometry.9

Within two hours, the thicknesses measured for the SAMs formed using one or

two eq. of Bu4NOH matched the predicted value (24.9 Å),53 indicating the

presence of a densely-packed monolayer comprising S-OPE3-SAc and S-OPE3-S.

The thicknesses measured for SAMs that were immersed for longer than two hours

were irreproducible and usually larger than the predicted value, which may

indicate the formation of multilayers as Tour et al. reported for NH4OH.1

Regardless of the cause, this observation means that SAMs formed from solutions

with Bu4NOH lack the reproducibility required for ME devices.

80

Figure 3.5 a. Ellipsometric thicknesses (Å) of the SAMs formed from 0.3 mM diSAc-OPE3 as function of the immersion time, with 0 eq. (black circles), 1 eq. (blue squares), 2 eq. (green diamonds), and 4 eq. of Bu4NOH (red triangles). SAMs with 1 and 2 eq. give reasonable thicknesses in about one hour. b. Ellipsometric thicknesses of the SAMs formed from 0.3 mM diSAc-OPE2, 0.3 mM diSAc-OPE3, and 0.1 mM diSAc-OPE4 with 0 eq. (after 45h, black circles), 1 eq. (after 70 min, blue squares), and 4 eq. of Bu4NOH (after 80 min, red triangles). Only the monolayers formed using 1 eq. Bu4NOH show an increase in thickness with the length of the molecule.


In the absence of Bu4NOH (zero eq.) we measured thicknesses of 14 Å after 100

min and 15 Å after 24 h, which is about 70% of the predicted value. This result

indicates that, as expected, diSAc-OPE3 can form monolayers without in situ

deprotection, but that these SAMs are not densely-packed (Figure 3.2a). Using

four eq. of Bu4NOH, we measured a thicknesses of only 10 Å, meaning that diS-

OPE3 forms worse monolayers than diSAc-OPE3. Upon immersing the Au

substrates in the solutions with four eq. of Bu4NOH, an orange precipitate formed

that we ascribe to the formation of insoluble disulfide precipitates. We observed

this precipitate in the NMR tube after exposure to oxygen (Figure 3.6). It is

unlikely, however, that micron-scale precipitates influence the formation of the

SAMs which happens on molecular length scale.

We found that the thicknesses of SAMs grown from diSAc-OPE2, diSAc-OPE3,

and diSAc-OPE4 solutions with four eq. Bu4NOH were independent of the length

of the molecule (~6 Å, see Figure 3.5b), whereas those from solutions with one eq.

Bu4NOH exhibited the expected length-dependence: 15, 20, and 51 Å respectively.

We ascribe the value of 51 Å for diSAc-OPE4 to multilayers.

81

Figure 3.6 a. 1H NMR spectra from 7.95-6.65 ppm, of 0.3 mM diSAc-OPE3 in THF-d8 (light gray), with addition of 6 eq. Bu4NOH (gray), and the same solution 24 h after the cap of the tube had been open for 20 seconds (thus after air exposure; a yellow precipitate was formed, black line). b. A structure of a disulfide to which we attribute the black NMR spectrum (larger disulfide oligomers are not visible in the NMR spectrum, due to precipitation).

Chapter 3

3.3.3 Deprotection by Triethylamine

The only report on using Et3N to form SAMs from acetyl thioesters of conjugated

dithiols is from Shaporenko et al.16,54 They observed densely-packed SAMs, but did

not describe the exact conditions used. This may be because the quality of SAMs

of OPEs formed using Et3N is much less sensitive to excess of base than, for

example, SAMs formed using Bu4NOH. We investigated the effects of the

concentration of Et3N on the formation of SAMs from diSAc-OPE2, diSAc-

OPE3, diSAc-OPE4, SAc-OPE2, and SAc-OPE3 by immersing Au substrates in

solutions of different concentrations of Et3N and 0.5 mM of each of these

compounds in THF (except diSAc-OPE4, which saturated above 0.1 mM) and

measuring the thicknesses of the resulting SAMs by ellipsometry.55 Using 3% (v/v)

Et3N with diSAc-OPE3, we observed reasonable thicknesses, but SAMs of diSAc-

OPE4 were too thin. For 9-15 % (v/v) Et3N we measured a linear increase in the

thicknesses of the SAMs with increasing length of molecules (Figure 3.7a), in

contrast to SAMs grown from solutions with Bu4NOH or without base (Figure

3.5b).

We followed the deprotection reaction using Et3N by acquiring UV-Vis spectra for

a 0.3 mM solution of diSAc-OPE3 in a 12% solution of Et3N in THF after 5

minutes, 24h, and 48h (Figure 3.7b). The spectrum did not change appreciably and

there were no peaks at 458 or 460 nm, indicating a lack of thiolate in solution.

82

Figure 3.7 a. A plot showing a linear increase of the thicknesses of SAMs of OPE-dithiols (blue structures, upper-left) and OPE monothiols (red structures, lower-right), formed after two days immersion time in solutions with 9-15% Et3N, with their length. SAMs of the OPE dithiols were measured by ellipsometry (blue circles) and those of OPE monothiols by ellipsometry (red filled squares) and XPS (black open squares). b. UV-Vis absorption spectra of 0.3 mM solution of diSAc-OPE3 in THF without base (black) and with 12% Et3N, after 1 day (blue) and 2 days (red).


Unlike Bu4NOH, Et3N is a hindered, non-nucleophilic base and therefore the

mechanism of the deprotection probably proceeds through the generation of a

ketene. Ketenes are normally generated by treating acid chlorides/bromides with a

non-nucleophilic base56,57 (e.g., acetyl chloride and Et3N) which abstracts an -αproton and eliminates chloride/bromide, reforming the carbonyl with a cumulative

double bond (Scheme 3.5). While thioesters normally do not form ketenes, here

the thiolate leaving-group is sufficiently delocalized to make it stable enough to

form a small amount of ketene (and the commensurate OPE thiolate).

Taking into account the fact that (loosely-packed) SAMs can form directly from

acetyl thioesters, we propose the following mechanism for the formation of SAMs

from diSAc-OPE3 and Et3N: diSAc-OPE3 adsorbs to the Au substrate where it is

slowly converted to SAc-OPE3-S-Au, eventually forming a very sparse monolayer

comprising small domains of standing-up phases, disordered phases, and lying-

down phases (which we observe as a smaller ellipsometric thickness than the

predicted value). The slow reaction between Et3N and diSAc-OPE3 in solution

produces an amount of SAc-OPE3-S that is small enough that effectively no diS-

OPE3 is formed. This small amount is below the detection limit of our UV-Vis

experiments. The SAc-OPE3-S that does form, however, associates strongly with

the Au substrate, displacing adsorbed diSAc-OPE3 and incorporating itself into

the standing-up phase, forming a densely-packed SAM as drawn in Figure 3.2c that

we observe as an ellipsometric thickness that equals the predicted value. These are

the ideal conditions for self-assembly because each step is highly-reversible: diSAc-

OPE3 forms a weakly-adsorbed lying-down phase and the low concentration of

SAc-OPE3-S prevents driving the equilibrium too far towards the (disordered)

chemisorbed state. Over the course of 24-48 h this process forms a high-quality,

densely-packed monolayer.

83

Scheme 3.5 The proposed mechanism for the reaction of a thioacetate with Et3N.

Chapter 3

3.3.4 Deprotection by Pyrrolidine

We have used pyrrolidine to hydrolyze the thioesters of diSAc-OPE3 in situ to the

thiol as described by Yelm.58 Since pyrrolidine is a strongly nucleophilic amine, it

most likely reacts with the thioester via an addition-elimination reaction as drawn

in (Scheme 3.6).

This mechanism is supported by the results of UV-Vis absorption and 1H NMR

experiments on 0.3-0.5 mM diSAc-OPE3 solutions in THF and THF-d8

respectively with one, two, and three eq. pyrrolidine added (Figure 3.8). Addition

of one eq. of pyrrolidine results in a redshift of the UV-Vis absorption spectrum by

3 nm (λmax shifts from 331 to 334 nm). Addition of a second eq. of pyrrolidine

causes λmax to shift to 336 nm, while addition of a third eq. does not influence the

spectrum. Thus diSAc-OPE3 reacts with two eq. pyrrolidine (one per SAc), in

agreement with the mechanism in Scheme 3.6.

1H NMR spectroscopy shows the signals of the product formed upon addition of

two eq. shifted upfield compared to diSAc-OPE3 (Figure 3.8b), but not as far as for

the dithiolate dianion (Figure 3.4c). Thus, we have formed a symmetric compound

other then the dithiolate dianion, most likely being the dithiol of OPE3.

Furthermore, we have identified N-acetylpyrrolidine in the 1H NMR spectrum,59

although we were not able to find the signal of the thiol (which could be

underneath the solvent signal of THF-d8).

We examined the influence of deprotection by pyrrolidine on the formation of

SAMs of diSAc-OPE3 on gold (Figure 3.9). SAMs from a solution with two eq.

pyrrolidine grow faster than from a solution with one eq. and reach completion in

about two days, which the SAMs from the solution with one eq. have not reached

after three days.

84

Scheme 3.6 The proposed mechanism for the reaction of a thioacetate with pyrrolidine.


However, SAMs grown from a solution to which 15% Et3N was added grow faster

than from solutions with pyrrolidine, even though for the solution with Et 3N no

difference of the UV-Vis spectrum was observed compared to the solution without

any base (i.e. diSAc-OPE3 was the main species present in the solution with Et3N).

This confirms our hypothesis that small amounts of monothiolate anions promote

the formation of SAMs, whereas SAMs from dithiols grow in a similar way as

those of dithioacetates, though the dithiols have the advantage that they can fit in

the vacancies better, so that the SAM reaches completion after about two days.

85

Figure 3.9 Ellipsometric thicknesses of the SAMs formed from diSAc-OPE3 as function of the immersion time, with 1 (blue squares), and 2 eq. of pyrrolidine (green diamonds), and 15% Et3N added (red circles).

Figure 3.8 a. UV-Vis absorption spectra of 0.3 mM diSAc-OPE3 in THF with 0 (black), 1 (blue), 2 (green), and 3 (red) eq. of Bu4NOH. b. 1H NMR spectra from 7.7-7.0 ppm, of 0.3 mM diSAc-OPE3 in THF-d8 (green), with addition of 1 eq. pyrrolidine (red), with addition of 2 eq. pyrrolidine (blue). These spectra indicate the formation of diSH-OPE3.

Chapter 3

3.3.5 Deprotection of Terphenylene Dithioacetate by Different Bases

In order to relate our results to previous studies that were done with NH4OH as

deprotecting agent for the dithioacetate of terphenylene (diSAc-P3), we measured

the UV-Vis absorption spectra of 0.3 mM diSAc-P3 in THF with zero, one, two,

three, four, and six eq. of Bu4NOH (Figure 3.10a). We compared these spectra to

those reported by Krapchetov et al. for 0.25 mM diSAc-P3 in THF using NH4OH.60

They found that a large excess of NH4OH (~640 eq.) was needed to affect the UV-

Vis absorption spectrum: the wavelength of the maximum absorption shifted from

301 to 312 nm after 25 h, which they attributed to formation of the thiolate. We

found that, as the peak at 301 nm diminished, one eq. of Bu 4NOH formed a peak

at 420 nm, which we assign to the monothiolate, and two to four eq. shifted it to

406 nm, which we assign to the dithiolate. Krapchetov et al. repeated the

experiment in ethanol and obtained UV-Vis spectra that more closely resemble

ours.

We observed only a 4 nm shift in the absorption spectrum upon addition of two

eq. pyrrolidine (Figure 3.10b), which we attribute to formation of the thiol instead

of the thiolate (Section 3.3.4). We postulate that NH4OH in THF forms SAc-P3-

SH, because of the aforementioned incompatibility of aqueous NH4OH with

aprotic solvents, but that SAc-P3-S and diS-P3 form in ethanol, a protic solvent,

stabilizing the thiolate by solvation. These results underscore the impact that

solvent can have on the effectiveness of the base on the deprotection of thioesters.

86

Figure 3.10 UV-Vis absorption spectra of 0.3 mM diSAc-P3 in THF a. with 0 (black), 1 (blue), 2 (green), 3 (orange), 4 (red), and 6 (dark red) eq. of Bu4NOH and b. without base (black), with 2 eq. of pyrrolidine (red), and with 15% of Et3N (blue).


When comparing NH4OH and Bu4NOH, even though the base is ostensibly the

same (OH–), the counterion determines the amount of reactive base that is present

in solution and thus the amount of thiolate that forms.

We repeated the measurements on the kinetics of the formations of SAMs with

diSAc-P3 and found the same trends as for diSAc-OPE3.55 Krapchetov et al.

observed similar trends for SAMs formed from diSAc-P3 on GaAs: low

concentrations of NH4OH in ethanol produce SAMs comprising mostly standing-

up phases, while high concentrations lead to more of the lying-down phases.61,60 No

high-quality monolayers were obtained from solutions with NH4OH in THF.62

Though they studied SAMs on GaAs, the relationship between the amount of

thiolate formed and the composition of the SAM is the same: pure thioester forms

low-density SAMs, a small fraction of monothiolate forms densely-packed SAMs,

and a high fraction of dithiolate forms only the lying-down phase.

3.4 Composition of the SAMs by XPSWe used X-ray Photoelectron Spectroscopy (XPS) to determine the composition of

SAMs formed from benzenethiol, SAc-OPE2, and SAc-OPE3.55 We found only

one S2p doublet at 162 eV for all of the SAMs formed from monothiols, indicating

that all of the sulfur atoms in the SAM are bound to Au. From the same data, we

estimated the thicknesses of the SAM by determining the ratio of the areas of the

peaks corresponding to C1s and Au4f and found good agreement with those

determined by ellipsometry (Figure 3.7a, see Section 3.8.4 for more details). We

varied the conditions of the formation of the SAMs from diSAc-OPE3 to

determine the influence of the ratios of diSAc-OPE3, SAc-OPE3-S, and diS-OPE3

that are present in solution. We measured SAMs formed from three solutions: 0.5

mM diSAc-OPE3 and i) no base, ii) 15% Et3N, and iii) six eq. Bu4NOH (Table 3.1

and Figure 3.11). We chose these three conditions because i serves as a control and

ii and iii are the boundary conditions for the formation of thiolate—no dithiolate

and no monothiolate, respectively. The thicknesses measured by XPS were 13.1 Å

for no base, 17.5 Å for 15% Et3N, and 9.8 Å for six eq. Bu4NOH—we observed the

same trend by ellipsometry (see notes of Table S2 for more details).

87

Chapter 3

The XPS spectra of the SAM formed without base shows two sulfur peaks, one

88

Figure 3.11 C1s (a, e, i, m, q), S2p (b, f, j, n, r), O1s (c, g, k, o, s), and N1s (d, h, l, p, t) XPS signals for SAMs from diSAc-OPE3 without base (a-d), with 15% Et3N (e-h), with 6 eq. Bu4NOH (i-l), without base, followed by immersion in 20 mM.Bu4NOH (m-p), with 15% Et3N, followed by immersion in 20 mM.Bu4NOH (q-t). Fits are shown as solid lines.


bound to Au (162 eV) and one unbound sulfur atom (164 eV). The integral of the

peak corresponding to the sulfur atoms that are bound to gold is smaller than that

for the unbound sulfur atoms because the signal for the buried sulfur atoms is

attenuated by the SAM. The integrals of the peaks corresponding to the carbon

(C1s, 288 eV) and oxygen (O1s, 532 eV) of the carbonyl are equal to that of

unbound sulfur (Table 3.1). We did not observe any other sulfur or oxygen peaks,

thus we conclude that the SAM comprises SAc-OPE3-S bound to Au. The SAM

formed using 15% Et3N again shows two unequal sulfur peaks (162 and 164 eV),

but the peak for S-Au was significantly smaller. This increased attenuation is again

due to the increase in the density of the SAM formed using 15% Et 3N compared to

that formed without base. The integral of the peak corresponding to the carbonyl

carbon (288 eV) is 70% of that of the oxygen (532 eV) and only 40% of that of

unbound sulfur. Since there are only two sulfur peaks (and no peaks for S=O at 168

eV), it is unlikely that this excess oxygen is from oxides of sulfur. By comparing the

integral of the peak corresponding to the carbonyl C1s to those of the carbon

atoms in the OPE backbone and the signal of unbound sulfur, we conclude that 40-

60% of the sulfur atoms that are not bound to Au are protected by acetyl groups.

(The presence of free thiols may be causing the apparent increase in the amount of

oxygen by inducing surreptitious, oxygen-rich compounds to adsorb to the surface.)

By comparison, Shaporenko et al. estimated this value to be 10-20% for SAMs of

diSAc-biphenyls.16 We could not identify any signals for nitrogen in the XPS data,

indicating that none of the Et3N was incorporated into the SAM.

The XPS data for SAMs formed using six eq. Bu4NOH show peaks for sulfur that

are too small to draw any conclusions from (other than the fact that there is not

much sulfur in the sample). No peaks corresponding to the carbon and oxygen of

the carbonyl are visible, but there is a large nitrogen peak. This means that the

SAMs formed from six eq. Bu4NOH (i.e., pure diS-OPE3) are not only significantly

less dense than the other two samples, but also incorporate the counter ion of the

base (ratio OPE : Bu4N+ ≈ 1). We treated the other two SAMs (no base and 15%

Et3N) with Bu4NOH and measured them again. The resulting spectra show thicker

SAMs with smaller signals for the carbonyl carbon and oxygen and the appearance

of a nitrogen peak. We conclude that Bu4NOH can be used to remove acetyl

thioesters from the surface of a SAM, but that Bu4N+ ions are incorporated into

the SAM (probably as counterions to the thiolates). Nevertheless, these results

show that we can not only determine the composition of head groups in SAMs

from dithioacetates, but that we can control this composition.

89

Chapter 3

Table 3.1 Composition of the SAMs: X-ray Photoelectron Spectroscopy Measurements

Conditions Integrated Intensities a Normalized Intensities

0.5 mM diSAc-OPE3 in THF

Au4f C1sCxHy

C1sC=O

S2pS-Au

S2pS-R

O1s N1s C1s per OPE C-atom b

84 eV 283-287 eV 288 eV 162 eV 164 eV 532 eV 403 eV 283-287 eV

no base, 70 h 13004 977 39 30 39 43 - 43

15% Et3N, 46 h 10845 1229 28 33 72 40 - 55

3 mM Bu4NOH, 40 min 12031 633 - 5 - - 17 17

(1) no base, 70h(2) 20 mM Bu4NOH, 80

sec c

7863 860 - 29 12 15 25 21

(1) 15% Et3N, 49 h(2) 20 mM Bu4NOH, 7

min c

5802 696 - 20 12 20 20 17

a. These areas are divided by the sensitivity factor: 1 for C1s, 1.79 for S2p, 2.49 for O1s, and 1.68 for N1s. For Au4f the total area is reported (not divided by a sensitivity factor)

b. The total area of the CxHy C1s signal is divided by the number of C-atoms in the OPE core. We correct for the presence of other C-atoms: (1) from the acetyl group, by assuming that the intensity of CH3 is the same as C=O, and (2) from Bu4N+, by assuming that the intensity of the N1s signal only comes from Bu4N+, and that the 16 C atoms of Bu4N+ each contribute with the same intensity to the C1s signal.

c. SAMs were prepared in two steps: the first step is the immersion in OPE-solution, the second step is the treatment with a 20mM Bu4NOH solution in THF (without OPE molecules).

3.5 Electrochemical Characterization of the SAMs

3.5.1 Quality of the SAMs

We measured the density of SAMs on Au discs formed from 0.3-0.5 mM diSAc-

OPE3 in THF and i) no base, ii) one eq. Bu4NOH, iii) four eq. Bu4NOH, and iv)

15 % (v/v) Et3N using cyclic voltammetry (CV). We acquired CV data for these

SAMs in a three electrode electrochemical cell with 0.1 mM aqueous K2SO4

electrolyte, containing a Fe2+/Fe3+ redox couple, using the Au discs as the working

electrode. We compared the redox waves to those for freshly cleaned Au (Figure

3.12). There were no redox waves present for SAMs formed using Et3N, indicating

that these SAMs were free of pinholes—i.e., they are densely-packed and high-

90


quality, covering 100% of the Au disc. Thus, with Et3N we meet the most

important requirement of SAMs for applications in Molecular Electronics: a

densely-packed and defect-free SAM reduces the formation of shorts.

The CV data for Au discs immersed in solutions comprising only Et3N (no OPE)

are identical to those for clean Au and have the largest current density (J, 175 and

180 A/cmμ 2 respectively). The second-largest J are for SAMs formed using no base

(132 A/cmμ 2) and four eq. Bu4NOH (136 A/cmμ 2). J is smaller for SAMs formed

using one eq. Bu4NOH (91 A/cmμ 2). These data agree with the data obtained

using ellipsometry and we can conclude that the thicknesses measured by

ellipsometry that were lower than the predicted values correspond to SAMs that

are less dense than 100% coverage.

3.5.2 Capacitance Measurements

In the same setup, in the absence of Fe2+/Fe3+, we measured the capacitance of

SAMs formed using 15% (v/v) Et3N in THF and 0.5 mM: i) benzenedithiol,63 ii)

diSAc-OPE2, iii) diSAc-OPE3, iv) diSAc-OPE4 (0.1 mM), and v) Au disks

immersed in 15% (v/v) Et3N in THF without OPEs as a control. We also

measured blank Au disks (Figure 3.13). In these CV measurements the SAM acts

as the dielectric layer for a capacitor that is formed from the dielectric double layer

91

Figure 3.12 Cyclic Voltammograms of 50 M FeKμ 3(CN)6 and 50 M FeKμ 4(CN)6 as a redox couple in 0.1M K2SO4 in water at 100 mV/s with Hg/HgSO4 as reference electrode, a Pt disk counter electrode, and gold disk working electrodes (0.44 cm2) with: diSAc-OPE3 and 4 eq. Bu4NOH (red), diSAc-OPE3 and 1 eq. Bu4NOH (blue), diSAc-OPE3 and 15% Et3N (green), diSAc-OPE3 without base (black), freshly cleaned gold (orange), and gold immersed in 15% Et3N in THF without OPE (gray). Only the SAM of diSAc-OPE3 formed using 15% Et3N completely blocks the Fe2+/Fe3+ redox signal, indicating a densely-packed SAM that is free of pinholes.

Chapter 3

and the Au disc. We measured a decrease in capacitance for increasing thicknesses:

9.56, 6.53, 4.38, and 2.57 F/cmμ 2 for v, i, ii, and iii respectively. A similar decrease

was reported for SAMs of alkanethiols64 and oligophenylenethiols,65 according

C/A = ε0 εr /d, in which C/A is the capacitance divided by the area, d is the

thickness of the SAM, ε0 is the electric constant and εr is the dielectric constant of

the SAM. Using this equation for the capacitances that we found for OPE1-3 gives

a dielectric constant of 5, which is slightly higher than expected.

The capacitance of the SAM formed from diSAc-OPE4 (2.47 F/cmμ 2) is nearly

identical to that from diSAc-OPE3 (2.57 F/cmμ 2). It is possible that this is the

result of defects in the SAMs, which give higher values for capacitance, but

unlikely given the close match between the predicted and measured values of

thickness by ellipsometry. This same trend was observed in LAMJs (see next

section).

92

Figure 3.13 a. Cyclic Voltammograms showing the capacitive current at 100 mV/s in 0.1 M K2SO4, using varying gold disk working electrodes: a reference gold sample immersed in 15% Et3N in THF (orange), with a SAM grown from benzenedithiol (black), from diSAc-OPE2 + 15% Et3N (blue), from diSAc-OPE3 + 15% Et3N (red), and from diSAc-OPE4 + 15% Et3N in THF (green), and b. Plot of the average capacitive current values (at -0.25 V vs Hg/HgSO4, which is +0.39 V vs SHE) versus the scan speed. The slopes of this plot give the capacitance values of the modified gold disk working electrodes.


3.6 Large Area Molecular Junction DevicesTo demonstrate the high-quality and high reproducibility of SAMs grown with

Et3N on large areas, we measured the current-densities (J, A/cm2) of SAMs of

benzenedithiol, diSAc-OPE2, diSAc-OPE3, and diSAc-OPE4 in LAMJs at an

applied bias of 0.5 V (Figure 3.16). These junctions comprise an evaporated Au

bottom electrode, the SAM, a layer of PEDOT:PSS that serves as the top-contact,

and a second evaporated Au electrode that is used to contact the PEDOT:PSS.66

The measured values of J are averaged over hundreds of devices with diameters of

5-50 m across two wafers for OPE1-3 and one wafer for OPE4. When μ plotted on

a logarithmic scale, these data are linear as a function of the thickness of the SAM.

Using the equation lnJ = J0 - d β (where β is the characteristic decay, d is the length

of the molecules in the SAM, and J0 is the theoretical current-density at d = 0) we

calculated β from the slope of OPE1-3 (Figure 3.16, black diamonds) to be 0.15

Å-1.67 Typical values of for thiol-terminated OPEs using STM break-junctionsβ

and CP-AFM are 0.34 and 0.21 Å-1 respectively,68,15 and are significantly lower than

those found for alkanethiols (0.6-0.73 Å -1 in LAMJs2,66 up to 0.9 Å-1 in many other

93

Figure 3.16 Average current densities at 0.5 V for Large-Area Molecular Junction devices with diameters ranging from 5 - 50 m. μ The right figure is a schematic (not to scale) of the architecture of the devices with OPE1-4 and the inset in the graph shows a 6 inch wafer with LAMJ devices (adopted from ref. 66). Black diamonds show the average current densities from two wafers each for optimized SAMs of benzenedithiol (0.5 mM in THF, without base), diSAc-OPE2 (0.5 mM in THF, 5-10% Et3N added), diSAc-OPE3 (0.5 mM in THF, 5-10% Et3N added), and diSAc-OPE3 (0.1 mM in THF, 10% Et3N added). The tunneling decay parameter β from the linear fit (black line) is 0.15 Å-1. Gray circles show the average current densities (one wafer each) of SAMs of diSAc-OPE3 grown under different conditions: 0.5 mM in THF without base gives a current densities that are higher than expected, 0.5 mM in THF with 10% Et3N gives the expected values, and 0.3 mM in THF with four eq. of Bu4NOH gives values that are much lower than expected; only SAMs formed using Et3N lead to reproducible data between experiments.



Chapter 3

junctions40). It is cumbersome to make a direct comparison to these valuesβ

because of the different areas (single-molecule for STM, hundreds of molecules for

CP-AFM, and areas of several µm for LAMJs) and contact geometries. However,

0.15 Å-1 is in good agreement with the value obtained for oligophenylenes in

LAMJs (0.26 Å-1)69 and in accordance with theoretical predictions (0.19 Å -1 for

OPEs and 0.24-0.33 Å-1 for oligophenylenes).70 For OPE4 we found a value very

close to that of OPE3 (log J = 2.33±0.29 A/cm2 for OPE4 (one wafer) vs

2.40±0.50 A/cm2 for OPE3), a trend also observed in the capacitance

measurements. The relatively high J of the SAMs of OPE4 might indicate the

presence of defects in the SAMs of OPE4 (inconsistent with the data obtained by

ellipsometry). Lu et al. observed a similar decrease in length dependence for a

diamine series of OPE1-7.71 They attribute this observation to a transition in the

charge transport mechanism from tunneling to a hopping between OPE3 and

OPE4, similar to the transitions reported by Frisbee for conductance

measurements on other types of SAMs.72

To demonstrate the intimate connection between the mechanism of deprotection

and the performance of ME devices, we measured J of SAMs of diSAc-OPE3 i)

without base (0.5 mM in THF, immersed for two days), ii) with four eq. Bu4NOH

(0.3 mM in THF, immersed for one hour) and iii) with 10% Et3N (0.5 mM in THF,

immersed for two days). These data are summarized in Figure 3.16 as gray circles.

The J that we measured for the SAM formed using Et3N is similar (within the error

bar) to the J found for identical SAMs in the length-dependence experiments

described above.73 For the SAMs without base we found a J that was a factor ten

higher which, in accordance with the lower apparent ellipsometric thickness, we

attributed to a less densely-packed SAM. The SAMs formed using Bu4NOH

resulted in devices with J two orders of magnitude lower than that of the SAMs

grown with Et3N. This is either due to the formation of multilayers, the presence of

Bu4N+, or the adsorption of polymerized disulfides on top of the SAM. Though we

do not know the exact structure of this layer, these electrical measurements

demonstrate that four eq. Bu4NOH gives SAMs of low quality. We note that in

these experiments, despite the poor quality of the SAMs formed without base and

using Bu4NOH, we obtained functional (i.e., non-shorted) devices that produced

reasonable values of J, highlighting the importance of using the correct procedures

to form SAMs for electrical measurements. Although it is common to assume that

high-quality, densely-packed SAMs form simply by treating a diSAc molecule with

any base, we show that it is not valid to conclude that a SAM is of high-quality

94


simply from the observation of "reasonable" data in a ME device.

3.7 ConclusionsWe draw two important conclusions from this work: i) densely-packed SAMs of

linear, conjugated dithiols only form from solutions that contain primarily

monothiolate and dithioacetate, but essentially no dithiolate, and ii) the

observation of reasonable data in ME devices is not sufficient evidence to conclude

that a SAM is densely-packed or of high-quality. The only way to achieve a

solution of monothiolate from diSAc molecules is to treat them with a base that

forms monothiolate in sufficiently low quantities that the effective concentration of

dithiolate in the solution is zero. We demonstrate unambiguously that this can be

done using 9-15% Et3N in THF and allowing (the high-quality) SAM to form over

24-48 h. Dense SAMs will also form with one or two eq. of Bu4NOH but, after

more than two hours of immersion, multilayers will form. The use of any amount

of Bu4NOH will lead to the incorporation of some Bu4N+ in the monolayer and

too much Bu4NOH will drive the equilibrium to the dithiolate, resulting in

monolayers that are not upright oriented SAMs, but chemisorbed molecules lying

flat on the surface. For some ME measurements it is not desirable to have a dense

monolayer. In these cases, diSAc molecules can be used without deprotection to

form reproducible, but not densely-packed SAMs with thioacetate head groups.

With this new understanding of the formation of SAMs we can exert some control

over the head group, which opens possibilities for new methods of contacting

SAMs. It is our hope that the use of these procedures will eliminate the quality of

the SAM as a variable in future work in ME and correct the tendency to under-

report the experimental details of the in situ deprotection of diSAc molecules.

95

Chapter 3


3.8.1 Synthesis

General Comments on Chemicals and Synthesis

Benzenedithiol was purchased from TCI (>95%) and benzene(mono)thiol from Aldrich (>99%).

DiSAc-P3 was synthesized by Bert de Boer.11 Tetrahydrofuran (THF) was dried by percolation over columns of aluminum oxide and R3-11-supported Cu-based oxygen scavengers, degassed,

and stored under nitrogen. THF-d8 was dried and degassed prior to use. Triethylamine (Et3N) was distilled over KOH under nitrogen or purchased from Fisher (HPLC grade) and degassed.

Diisopropylamine was distilled over NaOH. Copper iodide was heated and dried under vacuum and then stored under a nitrogen atmosphere. Tetrabutylammonium hydroxide 30-hydrate

(Bu4NOH) was purchased from Sigma-Aldrich and stored under dry nitrogen. All reactions were performed under a nitrogen atmosphere, using dry solvents and oven-dried glassware (150 °C).

UV-Vis absorption spectra were measured on a Perkin Elmer Lambda 900 Spectrometer in a 1 mm quartz cuvette with Teflon stopper, typically in 30-60 minutes after preparation of the

solution, unless indicated otherwise. J. Young NMR tubes were used for the deprotection experiments to keep the solutions under nitrogen during the measurement. Spectra were referred

to the solvent signal (CHCl3: H, 7.26 ppm; C, 77.0 ppm, THF-d8: H, 3.60 ppm). See Chapter 2 for more details on the analysis of organic compounds.

Bis[(4-tert-butylthiophenyl)acetylene (diStBu-OPE2)

Dichlorobis(triphenylphosphine)palladium(II) (92 mg , 0.13 mmol), copper iodide (43 mg, 0.23 mmol), and 2.11 (688 mg, 2.81 mmol)

were placed in a three-necked flask. THF (25 mL) and diisopropylamine (5 mL) were added and the mixture was stirred. 2.13 (960 mg, 3.85 mmol) was

added and the mixture was refluxed for 21 hours and concentrated to dryness. The crude product was redissolved in CH2Cl2 and run over a plug of silica gel, eluted with CH2Cl2. The resulting

1.29 g light brown solid was preadsorbed onto silica gel and purified by column chromatography (silica gel, CH2Cl2/heptane 1:4). The resulting material was recrystallized from 25 mL ethanol

and 593 mg (1.67 mmol, 60%) of the title compound was obtained as white crystals.1H NMR (400 MHz, CDCl3): 7.53-7.47 (m, 8H), 1.30 (s, 16H). δ 13C NMR (50 MHz, CDCl3): δ 137.24, 133.45, 131.48, 123.37, 90.28, 46.52, 30.97. IR (cm -1): 2972, 2960, 2939, 2919, 2894, 2858, 2162, 1925, 1594, 1497, 1479, 1468, 1457, 1398, 1362, 1163, 1143, 1105, 1094, 1012, 840,

831, 721, 657. HRMS (APCI) calculated for [M+H]+ 355.1549, found 355.1528. Calcd for C22H26S2: C, 74.52; H, 7.39; S, 18.09. Found: C, 74.89; H, 7.48; S, 18.31.

Bis[(4-acetylthiophenyl)acetylene (diSAc-OPE2)

diStBu-OPE2 (300 mg, 0.845 mmol) was dissolved in chloroform/toluene (1:1, 60 mL) and acetyl chloride (7.7 mL) was

96


added. While stirring, BBr3 (1 M in CH2Cl2, 15 mL, 15 mmol) was added slowly. The reaction

mixture was stirred for 3.5 hours and poured into ice water (600 mL). This was extracted with CH2Cl2 (4 x 200 mL), dried over Na2SO4, filtered, and all volatiles were removed by rotary

evaporation. The crude material was preadsorbed onto silica gel and purified by column chromatography (silica gel, CH2Cl2/heptane 2:1) yielding 250 mg (0.766 mmol, 91%) of the title

compound as a white solid.1H NMR (400 MHz, CDCl3): 7.57-7.54 (m, 4H), 7.42-7.39 (m, 4H), 2.44 (s, 6H). δ 13C NMR

(125 MHz, CDCl3): 193.38, 134.22, 132.22, 128.36, 124.12, 90.21, 30.30. IR (cmδ -1): 3372, 2922, 2852, 2187, 1909, 1691, 1395, 1350, 1120, 1103, 1090, 1013, 964, 826, 659, 616. HRMS

(APCI) calculated for [M+H]+ 327.0508, found 327.0484. Calcd for C18H14O2S2: C, 66.23; H, 4.32; S, 19.65. Found: C, 66.44; H, 4.72; S, 18.59.

1,4-Bis[(4-tert-butylthiophenyl)ethynyl]benzene (diStBu-OPE3)

This compound was prepared by a modification of the literature procedure.42 To a suspension of

dichlorobis(triphenylphosphine)palladium(II) (154 mg , 0.219 mmol) and copper iodide (105 mg, 0.551 mmol) in THF (25 mL) and toluene (25 mL)

were added triethylamine (21 mL), 2.13 (1.534 g, 8.06 mmol), and 1,4-diiodobenzene (887 mg, 2.69 mmol). The reaction mixture was stirred for 4.5 hours and poured into 500 mL NH4Cl in

water. This was extracted with CH2Cl2 (3 x 500 mL) and the combined organic layers were washed with brine (500 mL) and water (500 mL), dried over Na 2SO4, filtered, and the solvent

was removed under reduced pressure until crystallization started. The mixture was placed in the refrigerator overnight and the crystals were collected and washed with 12 mL cold diethylether.

The resulting solid was recrystallized from heptane and 905 mg (1.99 mmol, 74%) of the title compound was obtained as off-white crystals.1H NMR (300 MHz, CDCl3): 7.54-7.47 (m, 12H), 1.30 (s, 18H). δ 13C NMR (75 MHz, CDCl3): δ 137.26, 133.49, 131.57, 131.48, 123.31, 123.01, 90.78, 90.50, 46.55, 30.97. IR (KBr, cm -1): 2976,

2962, 2921, 2896, 2860, 2283, 2707, 2283, 1924, 1592, 1513, 1459, 1363, 1166, 1109, 1013, 840, 830, 537. HRMS (APCI) calculated for [M+H]+ 455.1862, found 455.1826.

1,4-Bis[(4-acetylthiophenyl)ethynyl]benzene (diSAc-OPE3)

This compound was prepared by a modification of the literature procedure.42 diStBu-OPE3 (302 mg, 0.665

mmol) was dissolved in chloroform/toluene (1:1, 60 mL) and acetyl chloride (6 mL) was added. While stirring, BBr3 (1 M in CH2Cl2, 12 mL, 12 mmol)

was added slowly. The reaction mixture was stirred for 4.5 hours and poured into ice water (500 mL). This was extracted with CH2Cl2 (4 x 200 mL), dried over Na2SO4, filtered, and all volatiles

were removed by rotary evaporation. The crude material was preadsorbed onto silica gel and purified by column chromatography (silica gel, CH2Cl2/heptane 2:1) yielding 210 mg (0.492

mmol, 74%) of the title compound as a white solid.1H NMR (500 MHz, CDCl3): 7.56 (d, δ J = 8.4, 4H), 7.52 (s, 4H), 7.41 (d, J = 8.4, 4H), 2.44 (s,

6H). 13C NMR (125 MHz, CDCl3): 193.37, 134.23, 132.17, 131.63, 128.33, 124.23, 123.01,δ 90.66, 90.59, 30.30. IR (cm-1): 3371, 2923, 2852, 2281, 1915, 1692, 1591, 1513, 1352, 1117, 1012,

964, 840, 832, 824, 619. HRMS (APCI) calculated for [M+H]+ 427.0821, found 427.0789.

97

Chapter 3

Bis(4-bromophenyl)acetylene (3.1)

In a Schlenk flask were placed dichlorobis(triphenylphosphine)-

palladium(II) (170 mg, 0.24 mmol), copper iodide (152 mg, 0.80 mmol), and 1-bromo-4-iodobenzene (2.23 g, 8.00 mmol). Benzene (40 mL), trimethylsilylacetylene

(0.390 g, 3.97 mmol), and DBU (7.2 mL) were added, directly followed by water (50 L). Theμ brown/orange mixture was stirred for 20 h. The mixture was poured into ether (550 mL) and

water (300 mL) while stirring vigorously. The organic layers were washed with water (3 x 100 mL), 10% HCl (3 x 100 mL), and brine (2 x 100 mL), and dried over NaSO 4 and filtered. The

solvent was removed in vacuum and the orange solid was purified by column chromatography (silica gel, heptane), which yielded 1.13 g (0.34 mmol, 85%) 3.1 as white crystals. 1H-NMR (400 MHz, CDCl3): 7.48 (d, δ J = 8.4, 4H), 7.38 (d, J = 8.4, 4H). 13C-NMR (100 MHz, CDCl3): 132.98, 131.68, 122.77, 121.86, 89.40. IR (KBr, cmδ -1): 3074, 2959, 2921, 1910, 1793,

1653, 1588, 1491, 1395, 1306, 1295, 1271, 114, 1073, 1006, 830, 822, 510.

Bis[4-((4-tert-butylthiophenyl)ethynyl)phenyl]acetylene (diStBu-OPE4)

In a three-necked flask were placed 3.1 (1.101

g, 3.28 mmol), dichlorobis(triphenyl-phosphine)palladium(II) (238 mg, 0.34

mmol), and copper iodide (65.8 mg, 0.35 mmol). THF (160 mL) and diisopropylamine (22 mL) were added and the mixture was stirred. 2.13 (1.52 g, 7.99 mmol) was added. The mixture was

refluxed overnight and became a white suspension. After removal of the solvent CH 2Cl2 (2 L) was added and the resulting solution was washed with water (2 x 500 mL) and brine (500 mL).

The organic layers were dried over Na2SO4, filtered, and the solvent was removed by rotary evaporation. The crude product was recrystallized from heptane/toluene, with hot filtration. The

obtained orange crystals (1.10 g) were recrystallized from toluene, which yielded 905 mg (1.63 mmol, 50%) of the title compound as light yellow crystals. 1H NMR (500 MHz, CDCl3): 7.5-7.48 (m, 16H), 1.31 (s, 18H). δ 13C NMR (125 MHz, CDCl3): δ 137.25, 133.55, 131.59, 131.57, 131.49, 123.32, 123.08, 122.98, 91.01, 90.85, 90.51, 46.55,

30.99. IR (cm-1): 2977, 2962, 2943, 2921, 2896, 2859, 2162, 1925, 1589, 1517, 1459, 1362, 1165, 1111, 1012, 837, 829, 722. HRMS (APCI) calculated for [M+H]+ 555.2175, found 555.2130.

Calcd for C38H34S2: C, 82.26; H, 6.18; S, 11.56. Found: C, 82.21; H, 6.19; S, 11.33.

Bis[4-((4-acetylthiophenyl)ethynyl)phenyl]acetylene (diSAc-OPE4)

diStBu-OPE4 (100 mg, 0.181 mmol) was

suspended in chloroform (57 mL) and toluene (27 mL) upon stirring and heating. After

cooling to room temperature acetyl chloride (9 mL) was added. BBr3 (1 M in CH2Cl2, 15 mL, 15 mmol) was added in portions and the reaction mixture was stirred for 4 days. It was poured into

ice water (600 mL), extracted with CH2Cl2 (4 x 200 mL), dried over Na2SO4, and filtered. The solution was concentrated until crystallization started. After cooling, crystals were filtered from

the brown solution, washed with toluene, and dried. The title compound was afforded as 41 mg (0.078 mmol, 43%) off-white solid.

1H NMR (400 MHz, CDCl3): 7.56 (d, J = 8.1, 4H), 7.52 (s, 8H), 7.41 (d, J = 8.0, 4H), 2.44 (s,δ

98


6H). 13C NMR (125 MHz, CDCl3): 193.50, 134.25, 132.17, 131.64, 131.57, 128.24, 124.20,δ

123.04, 122.90, 91.03, 90.65, 90.57, 30.33. IR (cm-1): 2919, 2202, 1927, 1694, 1590, 1518, 1485, 1409, 1396, 1351, 1112, 1093, 1012, 948, 839, 820, 620. HRMS (APCI) calculated for [M+H]+

527.1134, found 527.1090. Calcd for C34H22O2S2: C, 77.54; H, 4.21; S, 12.18. Found: C, 72.51; H, 3.92; S, 11.60.

1-tert-butylthio-4-[(phenyl)ethynyl]benzene (StBu-OPE2)

In a three-necked flask were placed 2.11 (1.017 g, 4.15 mmol), dichlorobis(triphenylphosphine)palladium(II) (163 mg, 0.23 mmol), and

copper iodide (48 mg, 0.25 mmol). THF (40 mL), diisopropylamine (8 mL), and phenylacetylene (618 mg, 6.05 mmol) were added. The mixture was refluxed for 21

hours, cooled to room temperature, and the solvents were evaporated under vacuum. The crude material was redissolved in CH2Cl2

and filtered over a plug of silica, eluted with CH2Cl2. The

resulting 1.3 g light brown solid was purified by column chromatography (silica gel, CH2Cl2/heptane 1:4) and recrystallized from ethanol (25 mL) resulting in 823 mg (3.09 mmol,

74%) of the title compound as white crystals. 1H NMR (400 MHz, CDCl3) 7.57-7.45 (m, 6H), 7.39-7.32 (m, 3H), 1.30 (s, 9H). δ 13C NMR (75

MHz, CDCl3) 137.21, 133.17, 131.60, 131.46, 128.42, 128.36, 123.62, 123.01, 90.84, 88.80,δ 46.45, 30.95. IR (cm-1): 2980, 2959, 2937, 2921, 2895, 2859, 2219, 1491, 1474, 1454, 1444, 1362,

1166, 1098, 1015, 917, 833, 755, 689. HRMS (APCI) calculated for [M+H] + 267.1202, found 267.1197. Calcd for C18H18S: C, 81.15; H, 6.81; S, 12.04. Found: C, 81.25; H, 6.81; S, 12.13.

1-acetylthio-4-[(phenyl)ethynyl]benzene (SAc-OPE2)

StBu-OPE2 (307 mg, 1.15 mmol) was dissolved in 50 mL chloroform/toluene (1:1) and acetyl chloride (5 mL) was added. BBr3 (1

M in CH2Cl2, 10.5 mL, 10.5 mmol) was added slowly and the reaction mixture was stirred for 4 hours and poured into 500 mL ice water. After stirring for 2 hours, this

was extracted with CH2Cl2 (500 mL in total), dried over Na2SO4, filtered, and all volatiles were removed. The crude product was purified by column chromatography (silica gel,

CH2Cl2/heptane, 2:1) yielding 245 mg (0.97 mmol, 84%) of the title compound as a yellow solid.1H NMR (400 MHz, CDCl3) 7.58-7.50 (m, 4H), 7.43-7.33 (m, 5H), 2.44 (s, 3H). δ 13C NMR (125

MHz, CDCl3) 193.49, 134.20, 132.15, 131.66, 128.53, 128.37, 127.97, 124.54, 122.87, 91.03,δ 88.58, 30.26. IR (cm-1): 2919, 2852, 2219, 1695, 1492, 1440, 1396, 1352, 1128, 1111, 1099, 1089,

1069, 1014, 940, 827, 755, 691. HRMS (APCI) calculated for [M+H] + 253.06816, found 253.06837. Calcd for C16H12OS: C, 76.16; H, 4.79; S, 12.71. Found: C, 76.20; H, 4.92; S, 12.52.

1-Bromo-4-[(4-tert-butylthiophenyl)ethynyl]benzene (3.2)

To a suspension of 1-bromo-4-iodobenzene (1.02 g, 3.59 mmol), dichlorobis(triphenylphosphine)palladium(II) (132 mg , 0.19 mmol),

and copper iodide (73 mg, 0.38 mmol) in THF (20 mL) and triethylamine (10 mL) was added 2.13 (682 mg, 3.58 mmol). The reaction mixture was stirred

for 24 hours at room temperature and poured into 500 mL NH4Cl in water. This was extracted with CH2Cl2 (3 x 300 mL) and the combined organic layers were washed with water (300 mL)

99

Chapter 3

and brine (300 mL), dried over Na2SO4, filtered, and the solvent was removed under reduced

pressure, yielding a red-brown solid. This solid was dissolved in CH2Cl2 and filtered over a plug of silica gel, eluted with CH2Cl2. The obtained 1.10 g orange solid was further purified by

column chromatography (silica gel, heptane/ CH2Cl2 4:1) and recrystallization from hexane, resulting in 620 mg (1.80 mmol, 50%) white crystals.1H NMR (400 MHz, CDCl3) 7.54-7.44 (m, 6H), 7.39 (d, J = 8.1, 2H), 1.30 (s, 9H). δ 13C NMR (100MHz, CDCl3): 137.24, 133.52, 133.01, 131.63, 131.43, 123.21, 122.67, 121.96, 89.92,δ

89.74, 46.51, 30.97. IR (KBr, cm-1): 2975, 2961, 2941, 2921, 2896, 2861, 2212, 1920, 1909, 1594, 1492, 1459, 1396, 1362, 1166, 1068, 1008, 839, 829, 743, 521. HRMS (APCI) calculated for

[M+H]+ 345.0307, found 345.0298. Calcd for C18H17BrS: C, 62.61; H, 4.96; S, 9.29. Found: C, 62.47; H, 4.93; S, 9.27.

1-[(4-tert-butylthiophenyl)ethynyl]-4-(phenylethynyl)-benzene (StBu-OPE3)

To a suspension of 3.2 (518 mg, 1.50 mmol), dichlorobis(triphenylphosphine)palladium(II) (361 mg , 0.51

mmol), and copper iodide (197 mg, 1.03 mmol) in THF (125 mL) and diisopropylamine (25 mL) was added phenyl acetylene (645 mg, 6.32 mmol). The

reaction mixture was refluxed for 27 hours, concentrated en redissolved in 200 mL CH2Cl2. This solution was washed with water (3 x 200 mL) and brine (200 mL), dried over Na2SO4, filtered,

and the solvent was removed under reduced pressure. The resulting black solid was purified by column chromatography (silica gel, CH2Cl2, and heptane/ CH2Cl2 4:1, gradually changing to

1:1). The 588 mg obtained solid was recrystallized from diethyl ether, resulting in 441 mg (1.20 mmol, 80%) of the title compound as white needles.1H NMR (400 MHz,CDCl3): 7.58-7.43 (m, 10H), 7.40-7.32 (m, 3H), 1.31 (s, 9H). δ 13C NMR (75 MHz,CDCl3): 137.23, 133.50, 131.61, 131.54 (multiple signals), 128.48, 128.39, 123.37,δ

123.30, 122.98, 122.82, 91.35, 90.66, 90.57, 89.04, 46.53, 30.99. IR (KBr, cm -1): 2981, 2963, 2938, 2922, 2896, 2861, 2213, 1923, 1676, 1513, 1363, 1168, 836, 757, 692, 526. HRMS (APCI)

calculated for [M+H]+ 367.1515, found 367.1507. Calcd for C26H22S: C, 85.20; H, 6.05; S, 8.75. Found: C, 85.29; H, 6.02; S, 8.78.

1-[(4-acetylthiophenyl)ethynyl]-4-[(phenyl)ethynyl]benzene (SAc-OPE3)

StBu-OPE3 (88 mg, 0.24 mmol) was dissolved in 18 mL chloroform/toluene (1:1) and acetyl chloride (2 mL) was

added. BBr3 (1M in CH2Cl2, 4 mL, 4 mmol) was added slowly and the reaction mixture was stirred for 3 hours and poured into 200 mL ice water. After stirring

for 1 hour, this was extracted with CH2Cl2 (3 x 150 mL), dried over Na2SO4, filtered, and all volatiles were removed. The crude product was purified by column chromatography (silica gel,

CH2Cl2/heptane, 1:1) yielding 74 mg (0.21 mmol, 88%) of the title compound as a yellowish solid.1H NMR (500 MHz, CDCl3) 7.58-7.53 (m, 4H), 7.52 (s, 4H), 7.41 (d, J = 8.4, 2H), 7.39 – 7.34δ (m, 3H), 2.44 (s, 3H). 13C NMR (125 MHz, CDCl3) 193.40, 134.23, 132.16, 131.62, 131.60,δ

131.55, 128.49, 128.38, 128.25, 124.28, 123.41, 122.96, 122.66, 91.40, 90.73, 90.40, 89.02, 30.30. IR (cm-1): 2921, 2852, 2214, 1695, 1505, 1440, 1395, 1353, 1177, 1127, 1104, 1069, 1014,

939, 838, 827, 755, 691. HRMS (APCI) calculated for [M+H]+ 353.0995, found 353.0983. Calcd

100


for C24H16OS: C, 81.79; H, 4.58; S, 9.10. Found: C, 80.29; H, 4.76; S, 8.69.

3.8.2 Preparation of the Substrates, SAMs, and Devices.

Substrates

Freshly cleaved mica was heated for 16 h at 375˚C in the vacuum chamber (10 -6-10-7 mbar) of a

custom-made thermal evaporator. 150 nm Au was evaporated at 0.05 nms -1 (30 s), 0.5 nms-1 (30 s), and then at 0.9 nms-1 until a thickness of 150 nm is reached. The substrates were heated for

one more hour after the deposition, then gradually cooled to room temperature over six hours, taken from the vacuum chamber, cut into pieces, and transferred into the glove box for

immersion in a thiolate solution. For the electrochemical measurements commercial 1 inch glass disks coated with 200 nm Au

were used (Ssens BV, Hengelo). These were cleaned with acidic Piranha (1 part 30% H 2O2 added to 3 parts 98% H2SO4; CAUTION DANGEROUS), rinsed with water and ethanol, and dried

with a nitrogen flow a prior to use.

Preparation of solutions and formation of SAMs

All solutions and SAMs were prepared inside a glovebox filled with nitrogen (<5 ppm O 2). THF

was used as solvent in all reported experiments. Solutions of diSAc-OPE4 were stirred and heated to 50°C, and filtered through a 1 m PTFE syringe filter by gravity prior to monolayerμ

growth. Samples were immersed upside down in the solution of diSAc-OPE4. After the given immersion time, samples were taken from solution and immersed three times in vials with clean

THF, after which the samples were dried in the glovebox or with a nitrogen pistol.

Large-Area Molecular Junctions

The Large Area Molecular Junctions were fabricated and measured by Tom Geuns and Paul van

Hal at Philips Research Laboratories in Eindhoven, as described by van Hal et al.,66 using MA1407 photoresist. SAMs were grown by immersion in 0.5 mM solutions in THF with Et3N

(for the acetyl protected compounds) for two days. The SAM of OPE4-DT was grown from a filtered 0.1 mM solution.

Electrochemistry

Electrochemical measurements were performed at the University of Twente with an Autolab PGSTAT10 in a three-electrode liquid cell, with the gold working electrode mounted at the

bottom of the cell (area as defined by an O-ring is 0.44 cm2), a platinum disk counter electrode, and a Hg/HgSO4 reference electrode (+0.64V vs SHE). Capacitance measurements were

performed in 0.1M K2SO4 in water at 50, 100, 200, 300, and 500 mV/s. The average between positive and negative current at -0.25V was determined from the fifth scan and plotted versus the

scan speed. The slope of this plot gives the capacitance. The packing density of the SAMs was studied in solution of 50 M FeKμ 3(CN)6 and 50 M FeKμ 4(CN)6 as redox couple in 0.1M K2SO4

in water by cyclic voltammetry at 100 mV/s.

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Chapter 3

3.8.3 EllipsometryWe determined the thicknesses of our SAMs by spectroscopic ellipsometry: a beam of linearly polarized light hits the surface with the SAM and is reflected. The polarization of this reflected

beam is changed by the surface with the SAM and this change is measured by the analyzer as the amplitude ratio (Ψ) and the phase difference (Δ) between the s- and p-components of the

polarized signal. Especially the phase difference is highly sensitive for the thickness of thin films. We acquired the ellipsometry measurements on a V-Vase Rotating Analyzer Ellipsometer from J.

A. Woollam Co., Inc. in air. Ψ and Δ were measured from 300-800 nm with an interval of 10 nm at 65, 70, and 75º angle of incidence.

The thickness of a SAM can be obtained from a fit. This fit requires the optical constants for the refractive index (index n and extinction coefficient k) as input. For every set of experiments we

measured a fresh gold-on-mica sample at three or four different spots. The data from these measurements were merged and the optical constants of our gold layer were fitted (the 150 nm

thick gold layer can be considered as infinite). We made a two-layer model for the fit of the measurements on the SAMs: a gold layer (with the optical constants as determined), with on top

a cauchy layer. Since we did not know the optical constants, we choose to use the values of n=1.551,11 and k=0 at all wavelengths (i.e. cauchy parameter A=1.55, B=C=0) and fit the

thickness. For every SAM we measured three different spots and reported the thicknesses as the average with the standard deviation as the error bar.

3.8.4 XPSXPS measurements were performed on a X-PROBE Surface Science Laboratories photoelectron

spectrometer with a Al K X-ray source (1486.6 eV) and a takeoff angle of 37º. We accumulatedα 20 scans for S2p, 10 for C1s, 10 for O1s, 15 for N1s, and 5 for Au4f. All reported data are

averaged over four different spots per sample. WinSpec74 was used to fit the recorded data with a background and minimum number of mixed Gaussian-Lorentzian singlets (C1s, N1s, O1s) or

doublets (Au4f; =3.67 eV, S2p; =1.18 eV) with a width of 1.21 eV.Δ ΔWe have determined the thicknesses of the SAMs from our XPS results by two different

methods: A) from the ratio between the carbon and the gold signals75 and B) from the attenuation of the gold signals:76

Method A

Thicknesses of the SAMs (dCS) are determined from the ratio of the areas of C1s and Au4f peaks by equation (1) with λAu = 31 Å, λC = 27 Å, dC = dCS - 1.8 Å (dC is the thickness of the

hydrocarbon layer without the thiolate); k is estimated to be 0.15 from XPS measurements on a SAM of undecanethiol on gold.

I C

I Au=k

1−exp −d C /C exp −d CS /Au

(1)

We determined dCS from IC/IAu by an iterative numerical approach. We should note that equation

(1) is valid for carbon-based thiols on gold (i.e. CxHyS-Au). Heteroatoms (N, O, and S not bound

102


to Au) that are present in the SAM do not contribute to the intensity of the carbon signal

(although they contribute to the attenuation of the gold intensity), so that slightly smaller thicknesses are expected to be found when heteroatoms are present.

Method B

Thicknesses (d) are determined from the attenuation of the Au4f signal by equation (2) with Au0

= 109754, = 42 Å, and = 37°.λ θ

I Au=I Au0 exp −d / sin (2)

Here we should note that in the set-up that we used the absolute intensities (or areas) of the XPS

signals depend on the alignment of the sample in the XSP chamber and the intensity of the X-ray beam. This is probably why some values calculated by this method differ significantly from

those obtained by ellipsometry and those obtained from equation (1). For this reason we consider the values obtained from the ratio between carbon and gold (method A) to be more

reliable, even though we cannot correct for the presence of heteroatoms there.

Table 3.2 Thicknesses of SAMs: results from X-ray Photoelectron Spectroscopy Measurements.

Molecule Conditions Measured Area

Thicknesses of the SAMs (Å)

0.4 - 0.6 mM OPE in THF Au4f C1s EllipsometryXPS

Method AXPS

Method B

diSAc-OPE3 no base, 70 h 65020 1016 13.3 13.1 13.2diSAc-OPE3 15% Et3N, 46 h 54227 1257 19.7 17.5 17.8diSAc-OPE3 3 mM Bu4NOH, 40 min 60156 633 4.7 9.8 15.2diSAc-OPE3 (1) no base, 70h

(2) 20 mM Bu4NOH, 80 sec39315 860 not

determined16.7 25.9

diSAc-OPE3 (1) 15% Et3N, 49 h(2) 20 mM Bu4NOH, 7 min

29010 696 17.9 17.9 33.6

benzene monothiol

no base, 42 h 96131 504 4.3 6.0 3.4

SAc-OPE2 13% Et3N, 42 h 76036 1107 11.3 12.4 9.3

SAc-OPE3 13% Et3N, 42 h 57315 1679 20.5 20.7 16.4

103

Chapter 3

3.9 References and Notes

1. J.M. Tour, L.R. Jones II, D.L. Pearson, J.J.S. Lamba, T.P. Burgin, G.M. Whitesides, D.L. Allara, A.N. Parikh, S.V. Atre, J. Am. Chem. Soc. 1995, 117, 9529-9534.

2. H.B. Akkerman, P.W.M. Blom, D.M. de Leeuw, B. de Boer, Nature 2006, 441, 69-72.



5. We define densely-packed as a SAM in which the thickness measured by ellipsometry is reproducibly within 80-100% of the maximum theoretical thickness (i.e., the length of the molecule + 2.3Å for the S-Au bond).

6. We define high-quality SAMs as being free of pinholes, as determined by electrochemical measurements.

7. J.C. Love, L.A. Estroff, J.K. Kriebel, R.G. Nuzzo, G.M. Whitesides, Chem. Rev. 2005, 105, 1103-1169.

8. W. Azzam, B.I. Wehner, R.A. Fischer, A. Terfort, C. Wöll, Langmuir 2002, 18, 7766-7769.

9. D.S. Seferos, D.A. Banach, N.A. Alcantar, J.N. Israelachvili, G.C. Bazan, J. Org. Chem. 2004, 69, 1110-1119.

10. K.H.A. Lau, C. Huang, N. Yakovlev, Z.K. Chen, S.J. O'Shea, Langmuir 2006, 22, 2968-2971.

11. B. de Boer, H. Meng, D.F. Perepichka, J. Zheng, M.M. Frank, Y.J. Chabal, Z. Bao, Langmuir 2003, 19, 4272-4284.

12. K. Walzer, E. Marx, N.C. Greenham, R.J. Less, P.R. Raithby, K. Stokbro, J. Am. Chem. Soc. 2004, 126, 1229-1234.

13. F. Maya, A.K. Flatt, M.P. Stewart, D.E. Shen, J.M. Tour, Chem. Mater. 2004, 16, 2987-2997.

14. A.J. Kronemeijer, H.B. Akkerman, T. Kudernac, B.J. Wees, B.L. Feringa, P.W.M. Blom, B. de Boer, Adv. Mater. 2008, 20, 1467-1473.

15. K. Liu, G. Li, X. Wang, F. Wang, J. Phys. Chem. C 2008, 112, 4342-4349.

16. A. Shaporenko, M. Elbing, A. Blaszczyk, C. von Hänisch, M. Mayor, M. Zharnikov, J. Phys. Chem. B 2006, 110, 4307-4317.

17. P.E. Colavita, P.G. Miney, L. Taylor, R. Priore, D.L. Pearson, J. Ratliff, S. Ma, O. Ozturk, D.A. Chen, M.L. Myrick, Langmuir 2005, 21, 12268-12277.

18. X. Zeng, C. Wang, A.S. Batsanov, M.R. Bryce, J. Gigon, B. Urasinska-Wojcik, G.J. Ashwell, J. Org. Chem. 2010, 75, 130-136.

19. L. Cheng, J. Yang, Y. Yao, D.W. Price Jr., S.M. Dirk, J.M. Tour, Langmuir 2004, 20, 1335-1341.

20. S. Berner, H. Lidbaum, G. Ledung, J. Åhlund, K. Nilson, J. Schiessling, U. Gelius, J. Bäckvall, C. Puglia, S. Oscarsson, App. Surf. Sci. 2007, 253, 7540-7548.

21. G.S. Ponticello, C.N. Habecker, S.L. Varga, S.M. Pitzenberger, J. Org. Chem. 1989, 54, 3223-3224.

22. C. Yu, Y. Chong, J. Kayyem, M. Gozin, J. Org. Chem. 1999, 64, 2070-2079.

23. M. Elbing, A. Blaszczyk, C.V. Hänisch, M. Mayor, V. Ferri, C. Grave, M.A. Rampi, G. Pace,

104

P. Samorì, A. Shaporenko, M. Zharnikov, Adv. Funct. Mater. 2008, 18, 2972-2983.

24. L. Cai, Y. Yao, J. Yang, D.W. Price Jr., J.M. Tour, Chem. Mater. 2002, 14, 2905-2909.

25. J.J. Stapleton, P. Harder, T.A. Daniel, M.D. Reinard, Y. Yao, D.W. Price, J.M. Tour, D.L. Allara, Langmuir 2003, 19, 8245-8255.

26. C.A. Hacker, J.D. Batteas, J.C. Garno, M. Marquez, C.A. Richter, L.J. Richter, R.D. van Zee, C.D. Zangmeister, Langmuir 2004, 20, 6195-6205.

27. S. Grunder, R. Huber, V. Horhoiu, M.T. González, C. Schönenberger, M. Calame, M. Mayor, J. Org. Chem. 2007, 72, 8337-8344; R. Huber, M.T. González, S. Wu, M. Langer, S. Grunder, V. Horhoiu, M. Mayor, M. Bryce, C. Wang, R. Jitchati, C. Schönenberger, M. Calame, J. Am. Chem. Soc. 2008, 130, 1080-1084; S. Wu, M.T. González, R. Huber, S. Grunder, M. Mayor, C. Schönenberger, M. Calame, Nat. Nanotechnol. 2008, 3, 569-574; S. Grunder, R. Huber, S. Wu, C. Schönenberger, M. Calame, M. Mayor, Eur. J. Org. Chem. 2010, 2010, 833-845.

28. A. Mishchenko, D. Vonlanthen, V. Meded, M. Burkle, C. Li, I.V. Pobelov, A. Bagrets, J.K. Viljas, F. Pauly, F. Evers, M. Mayor, T. Wandlowski, Nano Lett. 2010, 10, 156-163.

29. Y. Xia, G.M. Whitesides, Angew. Chem., Int. Ed. 1998, 37, 550-575.

30. Y. Loo, D.V. Lang, J.A. Rogers, J.W.P. Hsu, Nano Lett. 2003, 3, 913-917.

31. J.R. Niskala, W. You, J. Am. Chem. Soc. 2009, 131, 13202-13203.

32. F. Milani, C. Grave, V. Ferri, P. Samorì, M.A. Rampi, ChemPhysChem 2007, 8, 515-518.

33. K. Slowinski, H.K.Y. Fong, M. Majda, J. Am. Chem. Soc. 1999, 121, 7257-7261.



36. D.J. Wold, C.D. Frisbie, J. Am. Chem. Soc. 2001, 123, 5549-5556.


38. D. Scaini, M. Castronovo, L. Casalis, G. Scoles, ACS Nano 2008, 2, 507-515.

39. H. Haick, D. Cahen, Prog. Surf. Sci. 2008, 83, 217-261.


41. J.M. Tour, A.M. Rawlett, M. Kozaki, Y. Yao, R.C. Jagessar, S.M. Dirk, D.W. Price, M.A. Reed, C. Zhou, J. Chen, W. Wang, I. Campbell, Chem.-Eur. J. 2001, 7, 5118-5134.


43. R.P. Hsung, J.R. Babcock, C.E.D. Chidsey, L.R. Sita, Tetrahedron Lett. 1995, 36, 4525-4528.

44. M.J. Mio, L.C. Kopel, J.B. Braun, T.L. Gadzikwa, K.L. Hull, R.G. Brisbois, C.J. Markworth, P.A. Grieco, Organic Letters 2002, 4, 3199-3202.

45. For oliogophenylenes, which in general have a higher solubility compared to OPEs with the same number of phenyl rings, the solubility of quarterphenyldithioacetate was lower than that of quarterphenylmonothioacetate and too low for the formation of a SAM. For this reason “P4DT” is not included in ref. 69.

46. F. Schreiber, Prog. Surf. Sci. 2000, 65, 151-256.

105


47. G. Yang, G. Liu, J.Phys.Chem.B 2003, 107, 8746-8759.

48. SAc-OPE-SH molecules have been synthesized, but the mechanism is the same as SAc-OPE-SAc except that SH is cleaved faster than SAc by Au and is probably better in filling the defects of the SAM. see (a) A.K. Flatt, Y. Yao, F. Maya, J.M. Tour, J. Org. Chem. 2004, 69, 1752-1755, and A. Niklewski, W. Azzam, T. Strunskus, R.A. Fischer, C. Wöll, Langmuir 2004, 20, 8620-8624.

49. I. Um, J. Lee, S. Bae, E. Buncel, Can. J. Chem. 2005, 83, 1365-1371.

50. O.B. Wallace, D.M. Springer, Tetrahedron Lett. 1998, 39, 2693-2694.

51. We found that the HOMO of a thiolate anion attached to a OPE core is localized on the sulfur atom and the phenyl acetylene unit to which this sulfur atom is attached. The absorption of diS-OPE3 can therefore originate from two chromophores (separated by a phenyl ring), each of which resembles that on SAc-OPE3-S. However, in the case of diS-OPE2, these chromophores overlap and thus cause a shift of the spectrum of diS-OPE2 with respect to SAc-OPE2-S.

52. diS-OPE3 is probably present in the solution, however in quantities below the detection limit of 1H NMR (~ 5%)

53. The S-S distantance of diS-OPE3 is 19.8Å, corresponding to a maximum theoretical thickness of 24.9 Å for a SAM of AuS-OPE3-SAc and 22.1 Å for a SAM of AuS-OPE3-S.

54. In two other studies form the same group acetyl esters of monothiols are deprotected by Et3N: A. Shaporenko, K. Rössler, H. Lang, M. Zharnikov, J. Phys. Chem. B 2006, 110, 24621-24628; T. Weidner, K. Rössler, P. Ecorchard, H. Lang, M. Grunze, M. Zharnikov, J. Electroanal. Chem. 2008, 621, 159-170.

55. See supporting information to H. Valkenier, E.H. Huisman, P.A. van Hal, D.M. de Leeuw, R.C. Chiechi and Jan C. Hummelen, J. Am. Chem. Soc. 2011, 133, 4930-4939.

56. J.C. Sauer, J. Am. Chem. Soc. 1947, 69, 2444-2448.

57. E. Wedekind, Ber. Dtsch. Chem. Ges. 1901, 34, 2070-2077.

58. K.E. Yelm, Tetrahedron Lett. 1999, 40, 1101-1102.

59. 1H NMR (500 MHz, THF-d8) : 3.40 (t, J=7.0, 2H), 3.34 (t, J=7.0δ , 2H), 1.95-1.77 (m) and 1.91 (s, total s + m 7H).

60. D.A. Krapchetov, H. Ma, A.K.Y. Jen, D.A. Fischer, Y. Loo, Langmuir 2008, 24, 851-856.



63. No Et3N was added to the solution of benzenedithiol in THF.

64. M.D. Porter, T.B. Bright, D.L. Allara, C.E.D. Chidsey, J. Am. Chem. Soc. 1987, 109, 3559-3568.

65. E. Sabatani, J. Cohen-Boulakia, M. Bruening, I. Rubinstein, Langmuir 1993, 9, 2974-2981.


67. Including OPE4 in the fit gives =0.10Åβ -1.

68. See Chapter 4.

69. A.J. Kronemeijer, E.H. Huisman, H.B. Akkerman, A.M. Goossens, I. Katsouras, P.A. van

106

Chapter 3

Hal, T.C.T. Geuns, S.J. van der Molen, P.W.M. Blom, D.M. de Leeuw, Appl. Phys. Lett. 2010, 97, 173302; The β value of 0.26 Å-1 found for oligophenyelenes in LAMJs is smaller than those reported for other geometries.

70. H. Liu, N. Wang, J. Zhao, Y. Guo, X. Yin, F.Y.C. Boey, H. Zhang, ChemPhysChem 2008, 9, 1416-1424.

71. Q. Lu, K. Liu, H. Zhang, Z. Du, X. Wang, F. Wang, ACS Nano 2009, 3, 3861-3868.

72. S.H. Choi, B. Kim, C.D. Frisbie, Science 2008, 320, 1482-1486; S.H. Choi, C. Risko, M.C.R. Delgado, B. Kim, J. Bredas, C.D. Frisbie, J. Am. Chem. Soc. 2010, 132, 4358-4368.

73. We included this measurement on the SAM formed with Et3N as an internal control, since absolute values of current densities measured on LAMJs could vary between different batches of wafers.

74. WinSpec 2.09, developed at Laboratoire Interdépartemental de Spectroscopie Electronique, Namur, Belgium

75. J. Thome, M. Himmelhaus, M. Zharnikov, M. Grunze, Langmuir 1998, 14, 7435-7449.

76. C.D. Bain, G.M. Whitesides, J. Phys. Chem. 1989, 93, 1670-1673.

107


Chapter 3

108

Chapter 4Trends in the Conductances of Three Series of π-Conjugated Molecular Wires

This chapter describes the influence of length and HOMO-LUMO gap on the single molecule conductance of three series of oligo(phenylene ethynylene)-based molecular wires in Scanning Tunneling Microscopy-Break Junctions and compares the experimental trends with computational results. We found that the conductance is mainly determined by the length of the molecule: it decreases exponentially with the length of the molecule with a decay factor β of 0.33 Å-1. The conductance increases when the HOMO level of the molecular wire is closer in energy to the Fermi level of the gold electrodes.

109

Chapter 4

4.1 IntroductionIn Chapter 1 we have introduced our matrix approach to study the conductance of

series of π-conjugated molecules in a systematic way by different methods. In this

chapter we will present the results of the first type of conductance measurements

on three series of oligo(phenylene ethynylene)-based molecular wires (OPEs) in

which the structure varies systematically. The conductance of single molecules was

measured by the Scanning Tunneling Microscopy break-junction method (STM-

BJ).1 The substrate (gold) was repeatedly contacted with a STM tip (gold) in the

presence of a solution of molecular wires and the current was measured upon

withdrawal of the tip at constant bias voltage (Figure 4.1). We compare the

experimental results with calculations and discuss how the structure of the

molecular wires determines the conductance values in this method.

4.1.1 Single Molecule Conductance Studies on Series of π-Conjugated Molecules

Molecular electronics’ ultimate goal is to build electronic circuits out of molecules,

instead of conventional semiconductors and metals. To construct a functional

circuit of only molecules, we require both functional molecules and the

understanding of how these molecules function, besides the technological

challenges that we have to face. For this reason, incorporation of molecules as

active elements in more conventional electronics is currently a more realistic aim. 2

110

Figure 4.1 Schematic that shows the different series of molecular wires that we have measured in the Scanning Tunneling Microscopy-break junction setup, and that are described in this Chapter.

Trends in the Conductances of Three Series of π-Conjugated Molecular Wires

Many functional molecules have been proposed3 and synthesized.4,5 However, to

prove the functionality of a functional molecule is far from trivial,6 although

examples have been reported, for instance on light-induced conductance switching.7 The design of new functional molecules for molecular electronics requires the

fundamental understanding of how the charge transport properties of these

molecules depend on their structure. The absolute values of the conductance of

single molecules are hard to compare, when measured by different methods or in

different setups. Therefore, studying trends in the conductance values of series of

molecules is a more reliable approach.

In Table 4.1 we have listed examples of trends that have been found in single

molecule conductance studies on series of molecules. The conductance values

were derived from histograms of current-distance traces measured with

mechanically controlled break junctions (MCBJ),8,9 STM-BJ101112

-1314

15 or a related STM

technique.16,17 In most series, length dependence of the molecular conductance is

explored. The electrical conductance through molecular junctions is often found to

be a non-resonant tunneling process, generally described in the literature by

Equation 1. It describes how the molecular conductance (G) of the junction

decreases exponentially with the molecular length (L) while (A) is a constant that is

determined by the resistance of the contacts.

G=A⋅e−βL (1)

The decay constant tells how strong the conductance of the molecules decreasesβ

with the length. For short OPEs with amine anchoring groups a β of 0.20 Å-1 was

reported,10 whereas for amine-anchored oligophenylenes a larger β of 0.40 Å-1 was

found,11 in good agreement with calculations.18 Smaller values were reported forβ

oligoynes,16 Zn-porphyrin-containing wires,17 and oligothiophenes.13 Other studies

on series of π-conjugated molecules have shown that the conductance decreases

upon increasing oxidation potential, i.e., when the HOMO level is lower in

energy.12 Series of biphenyls with different torsion angles (Ф) have been studied

and it was found that the conductance increases with cos2Ф (i.e., smaller torsion

angles).11,14,15 For these series, the HOMO-LUMO gap decreases with increasing

cos2Ф,19 and the HOMO is likely to rise with decreasing Ф. MCBJ studies show

that substituents hardly influence the conductance values,8,9 which is in agreement

with theoretical studies.20,21 We can summarize these observations by stating that

the conductance values of π-conjugated molecules are mainly influenced by their

length and the HOMO level.

111

Chapter 4

Table 4.1 Examples of Trends in Conductance Measurements on Series of Molecules

Structure Parameter of investigation

Trends and Conductances

Ref.

1 Length =0.40 Åβ -1

496 nS for n=1 14 nS for n=3

11

2 Length n=0-2, =0.202 Åβ -1

n=2-6, =0.030 Åβ -1

178 nS for n=0 4.6 nS for n=6

10

3 Length =0.06 Åβ -1 16


2.1 nS for n=1 1.2 nS for n=2 0.6 nS for n=3

17


108 nS for n=1 3 nS for n=4

13

6 LengthEHOMO

Ox.potential↑→ G↓ G~e(-√(EHOMO-EAu)·L)

12

7 Torsion Angle(EHOMO)

G~cos2 Ф 119 nS for Ф=0 5.9 nS for Ф=88

11

8 Torsion Angle(EHOMO)

G~cos2 Ф 17 nS for Ф=17 0.7 nS for Ф=89

14

9 BackboneSubstituents

all OPVs: 16-17 nS

all OPEs: 9.3 nS

9

8

We studied the influence of both length and HOMO level on the electron transport

properties of OPE-based molecular wires with thiol anchoring groups. The trends

that are described above were mainly found for small molecules with amine

anchoring groups. It is not trivial that larger π-conjugated dithiolates should give

identical results, since the electronic coupling of thiols to gold is better compared

112


to amines,22 and the increased length could favor other transport mechanisms. We

therefore designed in 2008 the three families of OPE-based molecular wires that

are shown in Figure 4.1. In series I (4.1, 4.2, 4.3), we increased the molecular

length to find the effect on the single molecular conductance value by deriving

decay constant . In β series II (4.2, 4.4, 4.5), we decreased the HOMO-LUMO gap

by increasing the size of the π-conjugated system, while keeping the molecular

length constant. We replaced the middle phenyl ring of by a 1,4-disubstituted

naphthalene and a 9,10-disubstituted anthracene. We expected the HOMO level to

rise with the decreasing HOMO-LUMO gap. In series III (4.2, 4.6, 4.7), we again

replaced the middle phenyl ring by naphthalene and anthracene units, but now

substituted at the 2- and 6-positions. This series shows both an increase of the

molecular length and a decrease of the HOMO-LUMO gap. With this series we

aimed at determining the dominant effect.

4.2 Synthesis of the Molecular WiresWe synthesized the molecular wires that are shown in Figure 4.1 with acetyl

protected thiols (depicted with suffix A), because these are air-stable compounds

that can be deprotected to form thiolates in situ (see Chapter 3 for more details).

We followed the synthesis strategy as described in Chapter 2: the core of the wires

was made by a Sonogashira cross-coupling reaction in which the thiols were

protected as tert-butyl ethers (suffix B). In a second step, these were converted into

thioesters upon treatment with boron tribromide and acetyl chloride.

The synthesis of compounds 4.1A-4.3A is described in Chapter 3.2.1 (diSAc-

OPE2, diSAc-OPE3, and diSAc-OPE4 respectively) and that of 4.7A is given in

Chapter 2.2.2 (4.7A is 2.6A). Naphthalene containing wires 4.4B and 4.6B were

made according to the same procedure in good yields (67% and 72%) and

conveniently converted into 4.4A and 4.6A according to the method of Stuhr-

Hansen et al.23 in 83% and 76% respectively (Scheme 4.1).

The synthesis of 4.5A and B has been reported by Mayor et al.24 They first tried to

synthesize 4.5A by a Sonogashira cross-coupling of 9,10-dibromoanthracene with

4-ethynyl-1-thioacetylbenzene (2.10) and obtained 4.5A in only 5%. However, a

cross-coupling of 9,10-dibromoanthracene with 1-tert-butylthio-4-ethynylbenzene

(2.13) yielded 4.5B in 71%24,25 (we obtained 76% yield, after recrystallization). We

113

Chapter 4

have tried to convert 4.5B into 4.5A with 20 equivalents of BBr3, as used routinely.

These conditions did not only remove the tert-butyl protecting groups, but also

acetylated the anthracene core at the 2-position. We were not able to obtain pure

4.5A. Mayor et al. used only two equivalents of BBr3 and added this slowly to a

solution of 4.5B that was cooled to 0ºC, at small scale.24 Following this procedure,

we obtained a mixture of 4.5A, 4.5B, and 4.5 with one tert-butyl and one acetyl

protecting group. From this mixture we isolated 4.5A in 26% by column

chromatography. Attempts to convert 4.5B into 4.5A with a catalytic amount of

bromine25 (as used for several molecular wires described in Chapter 2) were not

successful. We have tried to synthesize 2.5B by another approach: a Sonogashira

cross-coupling of 9,10-dibromoanthracene with (triisopropylsilyl)acetylene,

followed by deprotection with TBAF and a subsequent Sonogashira cross-coupling

of the formed 9,10-bis(ethynyl)anthracene26 with 4-iodophenylthioacetate (2.8).

However, concentration of a solution of desilylated and purified 9,10-

bis(ethynyl)anthracene by rotary evaporation resulted in dark, insoluble crystals,27

minimizing the yield of desired product. Even though it should be possible to

prevent this to some extent, this synthetic pathway will probably not result in

significantly higher overall yields compared to the method of Mayor et al. These

difficulties that we encountered for the synthesis of 4.5A and not for the other

molecular wire are most likely due to the small HOMO-LUMO gap of 4.5A

(corresponding to a HOMO that is higher in energy and thus more reactive), as we

will see in the next sections.

114

Scheme 4.1 Syntheses of molecular wires 4.4-4.6: (i) Pd(PPh3)2Cl2, CuI, iPr2NH, THF, reflux; (ii) BBr3, AcCl, CHCl3, toluene.


4.3 Optical Properties and Energy Levels

4.3.1 UV-Vis Absorption Spectroscopy

The systematic variations in the structures of our molecular wires will influence

the energy levels of the compounds, which is reflected by their UV-Vis absorption

spectra (Figure 4.2). We determined the optical HOMO-LUMO gap from the low

energy onsets of the spectra (Table 4.2). UV-Vis absorption measurements on the

first series of molecular wires (4.1B, 4.2B, 4.3B) show only a slight decrease of the

optical HOMO-LUMO gap upon increasing length (3.7 eV for 4.1B to 3.4 eV for

4.2B and 3.2 eV for 4.3B). In the second series however (4.2B, 4.4B, 4.5B) the

length of the molecules is identical, where the HOMO-LUMO gap decreases

substantially from 3.4 eV for 4.2B to 3.0 eV for 4.4B and 2.5 eV for 4.5B. This

decrease is caused by the increase of the size of the π-system upon addition of

fused phenyl rings. The third series of molecules (4.2B, 4.6B, 4.7B) shows again a

small decrease of the HOMO-LUMO gap upon increasing length of the molecule

(3.3 eV for 4.6B and 2.9 eV for 4.7B).

The photoluminescence of compounds 4.2B-4.7B was measured and fluorescence

lifetimes of 0.5-1.8 10-9 s were found, indicating similar decay pathways for these

molecules.28

4.3.2 Energy Levels

As was explained in the introduction, both the length of the molecules and the

energy level of the HOMO influence the conductance of molecular wires,

115

Figure 4.2 Normalized UV-Vis absorption spectra of molecular wires 4.1B-4.7B as 10-5 M solutions in CH2Cl2.

Chapter 4

especially when anchored to gold electrodes via thiolates.29 We have performed

semi-empirical calculations, using the AM1-RHF method for structure

optimization on molecular wires with methyl-protected thiols. The obtained

lengths of the molecules and energies of the HOMO levels (EHOMO) are listed in

Table 4.2. These calculations are known to give accurate trends of EHOMO for a

series of molecules, however the absolute values from these calculations are not

reliable. We therefore have determined the EHOMO of a similar molecule (2.3) by an

Ultraviolet Photoelectron Spectroscopy (UPS) measurement and used these values

to correct all HOMO levels (see Chapter 2.5 for more information). We will use

these corrected levels in Section 4.5.2.

Table 4.2 Molecular Length and Energy Levels.

Wire HOMO-LUMO gap (eV) a

Length b calculated c (Å)

EHOMO calculated c (eV)

EHOMO corrected d (eV)

4.1 3.66 13.01 -7.880 -5.72

4.2 3.38 19.83 -7.970 -5.81

4.3 3.22 26.66 -8.017 -5.86

4.4 3.03 19.85 -7.895 -5.74

4.5 2.53 19.86 -7.647 -5.49

4.6 3.29 22.00 -7.968 -5.81

4.7 2.90 24.20 -7.900 -5.74

a. Determined from the onsets of the UV-Vis absorption spectra of the 4.#B compounds in CH2Cl2.b. The distance from S- to S-atom.c. HyperchemTM Release 7.52 for Windows Molecular Modeling Systems. Structures were optimized using the

AM1-RHF method. We used methyl-substituted thiols in the calculations.d. All levels were shifted by +2.16 eV to get agreement with the HOMO level as determined by the UPS

measurement in Chapter 2.

4.4 Conductance Measurements30

The conductance of the single molecules was investigated in a STM break junction

setup at the University of Bern.31 All measurements were performed by

Veerabhadrarao Kaliginedi and Pavel Moreno García. The molecular wires were

dissolved in mesitylene/THF (4:1) and placed in a liquid cell mounted on top of

an annealed gold sample. One equivalent of Bu4NOH was added to deprotect the

acetylated thiols and promote the formation of a self-assembled monolayer on the

gold surface (see Chapter 3). The setup was then brought in an argon atmosphere,

116


where the measurements were conducted (see Experimental Section 4.9.2 for

details).

The gold tip of the STM setup was repeatedly brought in contact with the gold

surface, and then withdrawn from the surface while the current was recorded.

Dividing this current by the bias voltage that was applied between the tip and the

surface gives the conductance of the junction (given in G0 = 2e2/h = 77.5 μS,

which is the conductance of one gold atom). Withdrawal of the tip resulted in elongation of the gold-gold junction and a decrease in the number of gold atoms in

the constriction, which caused the conductance to decrease from ~10 G0 to 1 G0

(Figure 4.3a), where the contact between tip and surface consisted of only one gold

atom. Upon further withdrawal, an abrupt decrease of the current was observed:

the “jump out of contact”. Then three types of curves were observed. 35-40% of

all curves showed an exponential decay of the tunneling current until the noise

level is reached (Type II, blue curves in Figure 4.3a). However, 40-60% of all

curves showed plateaus, which are attributed to molecular junctions (Type I, black

curves in Figure 4.3a). The remaining 10-15% of the curves was noisy, probably

due to mechanical instabilities (Type III, red curves in Figure 4.3a). About a

thousand of curves were combined (without any selection) and plotted in a two

dimensional (2D) histogram (Figure 4.3b), in which the x- and y-axes are the same

as in Figure 4.3a and the number of counts is shown on a color scale. The red area

in the top left part of the graph belongs to the gold-gold contact regime. The large

117

Figure 4.3 a. Examples of three types of conductance-distance traces for 4.2 at 100 mV bias with 58 nm/s stretching rate: Type I (black) curves with pronounced steps, Type II (blue) smooth exponentially decaying curves, and Type III (red) nonmonotonous, noisy curves. The curves are displaced over a certain distance for clarity. b. Two dimensional histogram of conductance -distance traces for 4.2 recorded at 100 mV bias without any data selection. The red spot in the histogram shows the plateau distribution. G1 and G2 indicate the high and low conductance plateaus. (Bern, note 30)

Chapter 4

red signature in the middle of the graph (G1) presents the plateaus caused by

molecules bridging the gap between the tip and the substrate. At the end of this

plateau, a light blue-green area can be found (G2). This is caused by a second

(smaller) plateau at lower conductance that is found in some of the traces (see inset

Figure 4.7a).

To compare the conductance values of molecular wires 4.1-4.7 the conductances

were plotted in conventional histograms for all three series (Figure 4.4). To

construct these histograms the number of data points was counted for each

conductance (current) value. When there is a plateau in the 2D histogram, then

this results in many counts at that particular conductance value and thus a peak in

the histogram. These peaks were fitted with a Gaussian distribution and the

maximum of this fit represents the most probable conductance value. These high

conductance values are given in Table 4.3 as G1. In the histograms of 4.1, 4.2, 4.4,

and 4.5 a low conductance (G2) feature is clearly visible and fitted with a

Gaussian.

The plateau lengths (x-axis of the 2D histogram) were analyzed in a similar way as

the conductance values (y-axis of the 2D histogram) and the obtained lengths are

given in Table 4.3. The conductance values were independent of the bias between

118

Figure 4.4 Conductance histograms for the three series of molecular wires, recorded at a bias of 100 mV and with 58 nm/s. The high and low conductance peaks (if present) are fitted with Gaussian distributions. (Bern, note 30)


tip and sample (65-300 mV) and of the speed with which the tip is withdrawn from

the substrate.32 However, the plateau lengths do depend on this stretching speed:

this length increases with increasing speed (in agreement with previous studies33).

We will return to this observation in Section 4.7.

Table 4.3 Conductance Values and Plateau Lengths. (Bern, note 30; Lancaster, note 53)

Wire Experimental Conductance (nS)

G1 G2

Plateau Length

(nm)

Calculated

Conductance (nS)a

4.1 114 ± 15 1.17 ± 0.28 0.71 ± 0.05 132

4.2 13.9 ± 1.1 0.76 ± 0.07 0.88 ± 0.07 25.6

4.3 1.22 ± 0.04 - 1.55 ± 0.16 6.3

4.4 20.8 ± 1.0 2.05 ± 0.25 1.37 ± 0.11 26.3

4.5 36.4 ± 1.8 1.65 ± 0.16 1.22 ± 0.02 68.2

4.6 4.12 ± 0.17 - 1.20 ± 0.05 13.2

4.7 3.61 ± 0.14 - 1.21 ± 0.05 11.6

a. See transport calculations in Section 4.6.

4.5 Discussion

4.5.1 Trends in the Conductance Values of Three Series of Molecular Wires

We have designed series I (Figure 4.1) as a series in which the length of the OPE

molecules increases with one phenylene ethynylene unit per molecule, from 13 to

20 to 27 Å. We thus mainly investigated the length dependence of the conductance

in this series, although with increasing length the HOMO-LUMO gap of π-

conjugated molecules decreases as well (Table 4.2). In Figure 4.4a we clearly see

that the G1 peak shifts to the left (i.e., to lower conductance) when going from 4.1

to 4.2 to 4.3 in series I. The G2 peaks shifts less, when we compare 4.1 and 4.2. It

might be that the G2 peak of 4.3 cannot be resolved, since this lower intensity

feature lays underneath the higher intensity G1 peak. We will return to these G2

features in Section 4.7. We have plotted the maxima as listed in Table 4.3 (G1) on

a logarithmic scale versus the length of the molecules in Figure 4.5a, in which

series I is given as black squares. We have fitted these three data points with

119

Chapter 4

Equation 1 (see Introduction 4.1.1) and found a clear exponential decay with a β of 0.33-0.34 Å-1. This value is higher than that for amine terminated OPEs (0.20

Å-1)10 and of thiolated OPEs measured in other configurations: 0.21 Å-1 by CP-

AFM,34 and 0.15 Å-1 by in large-area molecular junctions (see Chapter 3), but

identical to the value found in electrochemical electron transfer experiments.35

Molecule 4.2 (diSAc-OPE3) has been measured by several other groups, finding

similar values to the 13.9 nS that we found for the G1 main conductance peak: 13

nS,36 9 nS,8 and 10 nS.37 A value of 3.6 nS was obtained from less convincing

histograms.38 A conductance value for molecule 4.1 was reported by Xing et al.,37

who found 20 nS, which is much lower than our value of 114 nS, although they

found a β of 0.32 Å-1 when they used all three data points (benzene dithiol, 4.1,

and 4.2).

Series II was designed to investigate the influence of the HOMO-LUMO gap on

the conductance for molecules with identical length. In Figure 4.2 it was clearly

shown that this HOMO-LUMO gap decreases and in Figure 4.4b we find a slight

shift of the conductance peaks to higher values (G1 shifts from 14 to 21 to 36 nS).

Even though the anthracene-containing molecular wire 4.5 was studied before,24 it

is difficult to compare the absolute conductance value that we obtained from the

histogram with the reported derivative of few I-V curves. The trend that we

observe (i.e., higher conductance for a smaller optical HOMO-LUMO gap), could

be explained by the increase of the HOMO level with the decrease of the HOMO-

LUMO gap (see Table 4.2), which results in a better alignment with the Fermi

energy level of the gold electrodes (which is about -5 eV).39

In series III there is both an increase of length (as in series I) and a decrease of the

HOMO-LUMO gap (as in series II). Figure 4.4c shows a shift of the conductance

peaks from molecular wire 4.2 (14 nS) to 4.6 (4.1nS), although the difference

between 4.6 and 4.7 is only marginal (4.1 vs. 3.6 nS). These molecules thus have

smaller conductance values than 4.2, even though their HOMO-LUMO gaps are

smaller. The positions of the HOMO-levels are nearly identical within this series

(see Table 4.2), despite of the decrease of the HOMO-LUMO gap. The length of

this series does not increase as much as in series I (7 Å per molecule), only with 2 Å

per molecule. However, since the conductance decays exponentially with the

length, even a small increase of the length can count for a drastic decrease of the

conductance. In Figure 4.5a we see that the conductance values of series III are

positioned very closely to the fit of the length dependence of series I. We therefore

120


conclude that length dependence as in series I is the most prominent trend found in

series III. The trends found for series II and series III are similar to those found by

Venkataraman et. al. for diamino substituted acenes.40

4.5.2 A Simple Model for the Conductance of π-Conjugated Molecular Wires

In general, the tunneling current (J) through a rectangular barrier is described as

function of the width of barrier (z) by Equation 2:

J z ∝V⋅exp −4h 2m e⋅z (2)

in which V is the voltage applied over the junction, me is the effective electron mass,

and φ is the height of the barrier (h is Planck's constant). Dividing Equation 2 by

the voltage gives the following equation for the conductance (in the ohmic regime):

G z ∝exp −4h 2m e⋅z (3)

In a highly simplified model, we can describe the charge transport through our

121

Figure 4.5 Plot of the experimental conductance values versus (a) the length of the molecule: molecular wires 4.1, 4.2, and 4.3 (series I, black squares), 4.4 and 4.5 (series II, light gray triangles), and 4.6 and 4.7 (series III, dark gray diamonds), and (b) the length of the molecules times the square root of the offset between the Fermi level of gold and the HOMO level of the free molecule. The fits of the results are shown with the corresponding formula in both graphs. (note 30)

Chapter 4

gold-molecule-gold junction as tunneling through a rectangular barrier in which

the width of the barrier is the length of the molecule (calculated S-S distance, see

Table 1) and the height of the barrier is the difference between the Fermi level of

gold (EF) and the HOMO-level of the free molecule (EHOMO),12 without taking into

account broadening and shifting of these levels due the covalent bonding between

the sulfur atoms of the molecule and the gold electrode. A plot of our experimental

conductance values versus the length of the molecule times the square root of EF-

EHOMO is shown in Figure 4.5b. When comparing both plots in Figure 4.5, we find

that we have effectively moved the two data points from series II to the fitting line,

while the other data points are hardly affected.

We can extrapolate this simplified model for benzenedithiol. Semi-empirical

calculations in analogy to those in Section 4.3.2 give a length of 6.19 Å and EHOMO

of -5.61 eV. The model then predicts the conductance of benzenedithiol to be 931

nS, which is in good agreement with reported values: 924 nS,41 847 nS,42 and 369

nS.37

In conclusion, the measured data correspond with a simplified model of tunneling

through a rectangular barrier, in which the conductance is determined by the

length of the barrier (length of the molecule) and the height of the barrier (offset

between EHOMO and EF). This is in good agreement with the trends found for other

series of molecules, where we showed that EHOMO and length were the most

important parameters (see Table 4.1). However, this does not prove that such a

tunnel model, as described in more detail by Simmons et al.,43 is the best

description for charge transport trough molecular junctions.

4.6 Transport CalculationsThe trends in the conductance of our three series of molecules were investigated by

a computational chemistry approach: the transmission of electrons through the

different molecular wires attached to gold electrodes was calculated by Víctor M.

García-Suárez at Lancaster University. For this ab-initio calculations the

SMEAGOL code44 was used, which combines the non-equilibrium Green’s

function (NEGF) method with the Density Functional Theory (DFT) code

SIESTA.45 This code is suitable for electronic calculations on systems with many

atoms. The first results reproduced the experimental conductance trends, but

122


overestimated the absolute values by three orders of magnitude. This is because

DFT methods underestimate the HOMO-LUMO gap and, in this case, pinned the

HOMO at the Fermi energy level, which reduces the barrier significantly. For that

reason, a correction by a scissor-like operator was applied (SAiNT),46 by which the

HOMO was moved to lower energy and the LUMO to a higher energy, to get

agreement with the level that are given in Table 4.2. This resulted in HOMO levels

that are about 1 eV lower in energy than the Fermi energy of gold. The resulting

transmission T(E) as function of the energy of the electrons is shown in Figure 4.6.

Conductance values can be obtained by multiplying this T(E), with G0 (Figure 4.6e

and Table 4.3).

For the molecular wires of series I (Figure 4.6a and e) an exponential decrease of

T(E) (and thus of G) at E=EF was found with a β of 0.24 Å-1. The decrease of the

HOMO-LUMO gap can be seen as a decrease of the distance between the two

maximums of T(E). The first maximum is located around -1 eV for all molecules

of series I; this maximum corresponds to the HOMO level (the transmission is at a

maximum since the energy of the electrons corresponds to the energy level of the

HOMO, thus a very good alignment). The second maximum, that corresponds to

the LUMO, clearly shifts to a lower energy with the length of the molecular wires,

that increases from 4.1 to 4.2 to 4.3.

123

Figure 4.6 SAiNT corrected transmission curves calculated with SMEAGOL for the molecular wires 4.# of series I (a), series II (b) and series III (c). The molecules are contacted to two gold electrodes, in the hollow-adatom configuration (d). The conductance values at E = EF are plotted versus the length of the molecules (e). (Lancaster, note 53)

Chapter 4

For series II T(E) at E=EF is nearly identical for 4.2 and 4.4, while the transmission

of 4.5 is significantly higher and its HOMO-LUMO gap is smaller than that of the

other two molecules of series II. For series III we find a very good agreement

between the experimental and the computational trend in the conductance values:

the longer the molecule, the lower its conductance, although the differences

between the molecules are only small. The trends for the HOMO-LUMO gap of

series III are similar to that of series II. The gap of the naphthalene containing wire

(4.6) resembles that of 4.2, whereas the gap of the anthracene containing wire

(4.7) is smaller. The trends found for the conductance values by ab-initio

calculations thus follow the trends of the experimental G1 values very well, as can

be clearly seen by comparing Figure 4.6e and Figure 4.5.

4.7 A Molecule in a Breaking JunctionHaving investigated the trends in the conductance values for our three series of

molecular wires, we can look at the junction in more detail. In the previous

sections we focused on the high conductance (G1) values, without considering the

low conductance (G2) values observed in the traces and histograms (as shown in

Figure 4.7a for molecular wire 4.5) and the lengths of the plateaus. Therefore we

will now try to describe the dynamical binding of the molecule to the electrodes. It

is important to realize that the junctions are not static, instead they are

continuously formed and broken.

In the ab-initio calculations, the SAiNT correction for the HOMO-LUMO gap

only was not enough to obtain conductance values of the same order as the

experimental G1 values. The use of the asymmetric hollow-adatom configuration

(Figure 4.6d) resulted in a quantitative agreement between experimental and

computational results. In this configuration one sulfur atom is bound in the

threefold hollow site of the gold (111) surface (i.e., it binds to three gold atoms,

forming a pyramid). The other sulfur atom is bound to an adatom: a gold atom

that is bound to a gold (111) surface in the threefold hollow site. This hollow-

adatom configuration is reasonable for a molecule that is contacted to gold surface

(considered to be flat, though in reality relatively rough) and a STM tip with a

sharp apex, as drawn schematically in Figure 4.7b.

124


In the two dimensional histogram, we can see that the G1 plateau has a slope: the

most probable conductance value decreases with increasing distance between the

tip and the sample. This could be caused by the tilt angle of the molecule (θ) with

respect to the surface normal (Figure 4.7b). Withdrawal of the tip from the sample

could reduce this tilt angle as the junction stretches.47 When the tilt angle is large,

then the electronic overlap between the HOMO orbital (that is localized at the

sulfur atom and carbon backbone) and the gold surface is larger, which results in a

better coupling and higher conductance (Figure 4.8a).48 During the stretching of

the junction, the tilt angle decreases, resulting in a decrease of the conductance, as

observed in the two dimensional histogram.

This hypothesis that the tilted G1 plateau is originates from the reduction of the tilt

angle of the molecule in the junction is confirmed by the trend found in the plateau

lengths for the molecular wires (Table 4.3). These plateau lengths are shorter than

the length of the molecules. They increase with increasing molecular length for

series I and series III: for longer molecules the tip can be withdrawn further before

the molecule is oriented perpendicular to the surface. In series II the plateau length

is longer for molecular wires 4.4 and 4.5 compared to 4.2, which can be explained

by the larger tilt angle of molecules 4.4 and 4.5.49

As mentioned before, the plateau length increases with the stretching speed.33

When this speed is lower, stretching the junction takes more time and thermal

125

Figure 4.7 a. Two dimensional histogram of conductance-distance traces for 4.5 recorded at 100 mV bias without any data selection. The red spot in the histogram shows the plateau distribution. G1 and G2 indicate the high and low conductance plateaus. The inset shows examples of conductance-distance traces for 4.5 b. A highly simplified schematic representation of the configuration of molecular wire 4.2 attached to gold electrodes. The G1 plateau is attributed to the hollow-adatom configuration and the G2 plateau to the top-adatom (or adatom-adatom) configuration. (Bern, note 30)

Chapter 4

fluctuations are more likely to cause the junction to break before a 0° tilt angle is reached. When this junction breaks before it is stretched completely, the plateau length is obviously shorter.

After the tilt angle is reduced to 0°, the only way to further stretch the junction is by moving the binding site of the sulfur atom from the threefold hollow site to the top (or adatom) site (Figure 4.7b). Calculations showed that binding in the adatom-adatom

or adatom-top configuration results in lower conductance values compared to the

hollow-adatom configuration for a 0° tilt angle, see Figure 4.8. (In the top

configuration a sulfur atom is bound to one gold atom, that is part of the gold

(111) surface). Therefore, the second conductance value (G2) could be attributed to

a molecule that is bound in the adatom-adatom or adatom-top configuration, just

before the junction breaks. This is supported by the conductance-distance traces

that have both G1 and G2 plateaus (see inset Figure 4.7a).

In Figure 4.8 we have marked the different stages of the junction: after breaking of

the gold-gold contact, a molecular junction is formed in which the molecule is

bound in a hollow-adatom configuration, with a large tilt angle (“begin G1”).

Further withdrawal of the tip reduces this tilt angle, resulting in a slight decrease of

the conductance (towards “end G1”). Subsequently, the molecule moves to an

adatom-adatom or adatom-top configuration with a significantly lower

conductance (“G2”), after which the junction breaks.

126

Figure 4.8 SAiNT corrected transmission curves calculated with SMEAGOL for the molecular wire 4.2, in the hollow-adatom configuration (a) and the adatom-adatom configurations (b) for tilt angles of 0 and 80°. The subsequent stages of the junction are marked. (Lancaster, note 53)


4.8 ConclusionsWe have designed and synthesized three series of π-conjugated molecular wires

with varying length and HOMO-LUMO gap. The conductance of these molecules

was studied in a STM-break junction setup and the conductance decreased

exponentially with increasing molecular length, with a decay constant of β of 0.33

Å-1. Furthermore, we discovered that the conductance increases with a decreasing

HOMO-LUMO gap, i.e., when the HOMO is higher in energy and the offset

between the HOMO level of the molecule and the Fermi level of the gold

electrodes is smaller. These findings are well described by a simple model for

tunneling through a rectangular barrier, in which the dimensions of this barrier are

given by the length of the molecule and the mentioned offset. The experimental

results are in good agreement with the results of ab-initio transport calculations.

The combination of these calculations and the two dimensional histograms from

the STM-break junction experiments resulted in a possible description of the

formation and breaking of the junction, including the different contact geometries,

which result in two different conductance plateaus for the molecular wires with

conductance values larger than 5 nS.

Concerning the structural design rules for linear conjugated OPE-based molecules,

we have to conclude that the length of the molecule mainly determines its single

molecule conductance at low voltages and that the energy of the HOMO level (or

HOMO-LUMO gap) has only a minor influence.

127

Chapter 4


4.9.1 Synthesis

General Comments on Chemicals and Synthesis

All reactions were performed under a nitrogen atmosphere, using oven-dried glassware (150°C)

and dry solvents. Diisopropylamine was distilled over NaOH. Copper iodide was heated and dried under vacuum. See Chapter 2 for the synthesis of 1-tert-butylthio-4-ethynylbenzene (2.13)

and details on the analyses of organic compounds.

1,4-Bis[(4-tert-butylthiophenyl)ethynyl]naphthalene (4.4B)

To a suspension of 1,4-dibromonaphthalene (457 mg,

1.60 mmol), dichlorobis(triphenylphosphine)-palladium(II) (113 mg , 0.16 mmol), and copper iodide

(30.5 mg, 0.16 mmol) in THF (90 mL) were added diisopropylamine (16 mL) and 2.13 (772 mg, 4.05 mmol). The reaction mixture was refluxed for

16 hours, concentrated, and run over a plug of silica gel, with CH2Cl2 as the eluent. The crude material was purified by column chromatography (silica gel, CH2Cl2/heptane 1:4) and

recrystallized from heptane, yielding 541 mg (1.07 mmol, 67%) of the title compound as light yellow crystals.

1H NMR (400 MHz, CDCl3): 8.47-8.45 (m, 2H), 7.74 (s, 2H), 7.67-7.65 (m, 2H), 7.62-7.56δ (m, 8H), 1.33 (s, 18H). 13C NMR (125 MHz, CDCl3): 137.33, 133.69, 133.00, 131.55, 129.78,δ

127.35, 126.59, 123.47, 121.46, 95.52, 88.95, 46.60, 31.01. IR (cm-1): 2970, 2959, 2936, 2918, 2892, 2858, 2170, 1568, 1507, 1482, 1384, 1365, 1359, 1161, 1148, 1097, 1016, 834, 762, 695.

HRMS (APCI) calculated for [M+H]+ 505.2018, found 505.1978. Calcd for C34H32S2: C, 80.90; H, 6.39; S, 12.71. Found: C, 81.05; H, 6.38; S, 12.85.

1,4-Bis[(4-acetylthiophenyl)ethynyl]naphthalene (4.4A)

4.4B (302 mg, 0.598 mmol) was dissolved in chloroform/toluene (1:1, 60 mL) and acetyl chloride (6

mL) was added. While stirring, BBr3 (1 M in CH2Cl2, 12 mL, 12 mmol) was added slowly. The reaction mixture

was stirred for 4 hours and poured into ice water (500 mL). This was extracted 3 times with CH2Cl2 (500 mL), dried over Na2SO4, filtered, and all volatiles were removed by rotary

evaporation. The crude material was preadsorbed onto silica gel and purified by column chromatography (silica gel, CH2Cl2/heptane 1:1) yielding 235 mg (0.493 mmol, 83%) of the title

compound as a yellowish solid.1H NMR (500 MHz, CDCl3): 8.46-8.44 (m, 2H), 7.75 (s, 2H), 7.75-7.66 (m, 6H), 7.46 (d, δ J =

8.2, 4H), 2.46 (s, 6H). 13C NMR (125 MHz, CDCl3): 193.49, 134.34, 132.96, 132.22, 129.85,δ 128.38, 127.43, 126.54, 124.32, 121.38, 95.26, 89.08, 30.35. IR (cm -1): 3377, 3060, 2921, 2852,

128


2201, 1912, 1692, 1591, 1486, 1395, 1354, 1113, 1094, 1014, 957, 825, 758, 699, 617. HRMS

(APCI) calculated for [M+H]+ 477.0977, found 477.0942. Calcd for C30H20O2S2: C, 75.60; H, 4.23; S, 13.46. Found: C, 75.75; H, 4.38; S, 13.29.

9,10-Bis[(4-tert-butylthiophenyl)ethynyl]anthracene (4.5B)

This compound was prepared by a modification of the literature procedure.24 To a suspension of 9,10-

dibromoanthracene (540 mg, 1.61 mmol), dichlorobis(triphenylphosphine)palladium(II) (115 mg ,

0.163 mmol), and copper iodide (36.7 mg, 0.193 mmol) in THF (80 mL) were added diisopropylamine (16 mL) and 2.13 (803 mg, 4.22 mmol). The

reaction mixture was refluxed for 23 hours and, after cooling to room temperature, poured into 350 mL water. The mixture was extracted with CH2Cl2 (3 x 100 mL) and the combined organic

layers were washed with water (4 x 200 mL) and brine (200 mL), dried over Na2SO4, filtered, and the solvent was removed under reduced pressure. The resulting solid was purified by column

chromatography (silica gel, CH2Cl2) and recrystallized form toluene to yield 676 mg (1.22 mmol, 76%) of the title compound as yellow crystals.

1H NMR (400 MHz, CDCl3): 8.70-7.67 (m, 4H), 7.74 (d, δ J = 8.0, 4H), 7.75-7.62 (m, 8H), 1.35 (s, 18H). 13C NMR (100 MHz, CDCl3): 137.42, 133.85, 132.11, 131.54, 127.21, 126.95,δ

123.68, 118.42, 101.97, 87.94, 46.68, 31.04. IR (cm-1): 3058, 2956, 2859, 2198, 1925, 1482, 1397, 1363, 1168, 1148, 1014, 832, 763, 727, 640. HRMS (APCI) calculated for [M+H]+

555.2175, found 555.2131.

9,10-Bis[(4-acetylthiophenyl)ethynyl]anthracene (4.5A)

This compound was prepared according to the literature

procedure.24 4.5B (201 mg, 0.36 mmol) was dissolved in chloroform/toluene (1:1, 25 mL), cooled to 0°C, and

acetyl chloride (1 mL) was added. While stirring at 0°C, BBr3 (1 M in CH2Cl2, 0.71 mL, 0.71 mmol) was added

slowly. After removal of the ice-salt bath, the reaction mixture was stirred for 4.5 hours and poured into ice water (500 mL). This was extracted with CH2Cl2 (3 x 200 mL), dried over

Na2SO4, filtered, and all volatiles were removed by rotary evaporation. The crude material was preadsorbed onto silica gel and purified by column chromatography (silica gel, CH2Cl2/heptane,

gradually increasing from 1:1 to 2:1) yielding 50 mg (0.095 mmol, 26%) of the title compound as an orange solid.

1H NMR (500 MHz, CDCl3): 8.68-8.66 (m, 4H), 7.81 (d, δ J = 8.2, 4H), 7.67-7.65 (m, 4H), 7.51 (d, J = 8.2, 4H), 2.48 (s, 6H). 13C NMR (125 MHz, CDCl3): 193.38, 134.44, 132.21, 132.13,δ

128.58, 127.17, 127.03, 124.53, 118.37, 101.69, 88.10, 30.35. IR (cm-1): 3060, 2920, 2852, 2199, 1691, 1589, 1483, 1395, 1118, 1095, 954, 823, 759, 726, 633. HRMS (APCI) calculated for

[M+H]+ 527.1134, found 527.1093.


In a three-necked flask were placed 2,6-

129

Chapter 4

dibromonaphthalene (527 mg, 1.84 mmol), dichlorobis(triphenylphosphine)palladium(II) (140

mg, 0.20 mmol), and copper iodide (47 mg, 0.25 mmol). THF (96 mL), diisopropylamine (19 mL), and 2.13 (920 mg, 4.83 mmol) were added. The mixture was refluxed for 23 hours, cooled

to room temperature, and poured into water (200 mL). This was extracted with CH2Cl2 (3 x 100 mL). The organic layers were washed with water (4 x 400 mL) and brine (400 mL), dried over

Na2SO4, filtered, and the solvent was evaporated under vacuum. The crude brown solid was preadsorbed onto silica and purified by column chromatography (silica gel, CH2Cl2/heptane

1:1). The resulting material was recrystallized from toluene (30 mL), resulting in 640 mg (1.3 mmol, 72%) yellow crystals. 1H NMR (400 MHz, CDCl3): 8.04 (s, 2H), 7.80 (d, δ J = 8.4, 2H), 7.60 (d, J = 8.4, 2H), 7.54 (s, 8H), 1.31 (s, 18H). 13C NMR (50 MHz, CDCl3): 137.27, 133.49, 132.42, 131.55, 131.30,δ

129.13, 127.91, 123.48, 121.29, 91.08, 90.00, 46.54, 31.00. IR (cm -1): 2968, 2960, 2938, 2922, 2897, 2859, 2210, 2164, 1927, 1597, 1480, 1470, 1449, 1359, 1169, 1150, 1097, 1013, 894, 834,

819, 665. HRMS (APCI) calculated for [M+H]+ 505.2018, found 505.1979. Calcd for C34H32S2: C, 80.90; H, 6.39; S, 12.71. Found: C, 80.26; H, 6.34; S, 12.64.


4.6B (215 mg, 0.425 mmol) was dissolved in chloroform/toluene (1:1, 40 mL) and acetyl chloride

(4 mL) was added. While stirring, BBr3 (1 M in CH2Cl2, 8 mL, 8 mmol) was added slowly. The

reaction mixture was stirred for 3.5 hours and poured into ice water (400 mL). This was extracted with CH2Cl2 (4 x 200 mL), dried over Na2SO4, filtered, and all volatiles were removed

by rotary evaporation. The crude material was redissolved in CH2Cl2 and purified by column chromatography (silica gel, CH2Cl2/heptane, gradually increasing from 1:1 to 2:1) yielding 155

mg (0.325 mmol, 76%) of the title compound as a light yellow solid.1H NMR (500 MHz, CDCl3): 8.03 (s, 2H), 7.79 (d, δ J = 8.4, 2H), 7.60 (d, J = 8.0, 6H), 7.42 (d,

J = 8.1, 4H), 2.45 (s, 6H). 13C NMR (125 MHz, CDCl3): 193.39, 134.24, 132.41, 132.21,δ 131.40, 129.12, 128.23, 127.93, 124.36, 121.17, 91.24, 89.76, 30.29. IR (cm -1): 3374, 3034, 2921,

2162, 1915, 1695, 1598, 1484, 1395, 1355, 1119, 1108, 1099, 1087, 1015, 956, 893, 831, 823, 814, 630. HRMS (APCI) calculated for [M+H]+ 477.0977, found 477.0941. Calcd for

C30H20O2S2: C, 75.60; H, 4.23; S, 13.46. Found: C, 75.44; H, 4.19; S, 13.51.

4.9.2 Conductance Measurements30

Sample Preparation

The conductance of single molecule junctions was studied at room temperature using a modified molecular imaging PicoSPM. The sample electrodes were Au(111) disks of 2 mm height and 10

mm in diameter, or Au on silicon samples of 1x1 cm2. The Au substrates were flame annealed prior to use and mounted on the sample holder.

Molecules 4.1A-4.7A were dissolved on air in a 4:1 mixture of 1,3,5-trimethylbenzene (mesitylene) and tetrahydrofuran (THF) at 0.1 mM. 100 L of this solution was added to theμ

liquid cell (Kel-F) that was mounted on top of the sample. The thiols were deprotected inside

130


this liquid cell by addition of 10-15 L 1 mM tetrabutylammonium hydroxide (Buμ 4NOH)

solution in THF. The setup was then placed in a custom-made gas-glass chamber, filled with high-purity argon (CarbaGas, 99.999%) and purged for 5-10 min to prevent oxygen exposure

(that results in disulfide formation) and contamination from air.The STM tips were uncoated, electrochemically-etched gold wire (99.999%, 0.25 mm diameter,

etching solution 1:1 mixture of 30% HCl and ethanol).50

Electronics

The standard STM scanner was replaced with a modified, dual-channel preamplifier.51 The input

current was simultaneously converted to two voltage signals (range ±10 V) with conversion factor 21µA/V (high range) and 10 nA/V (low range). Both signals were split, and the original as

well as 10 times amplified signals were recorded. The current was measured in an extraordinary wide range of 1 pA to 150 µA with high resolution. The non amplified low range current signal

was fed back to the STM controller, preserving original the STM imaging capability of PicoSPM.

The current-distance measurements were performed with a separate, home-built analog ramp unit (PC + National Instruments PCI-6040E I/O card + analog ramp circuit + lab made

software). It was connected to a lab-made break box, wired between the STM controller and the measuring head. This arrangement enabled the controlling software to read out current signals as

well as to control the vertical position of the tip by feeding the voltage to piezo element driving the vertical tip movement. The data was collected with a digital oscilloscope Yokogawa DL750

(16bit, 1 MS s-1).The STM tip was brought to a preset tunneling position typically defined by iT =0.1 nA.

Subsequently the STM feedback was switched off, and the tip approached the substrate with the molecules at constant x-y position. The approach was stopped when a predefined upper limit

was reached (<10 G0). At this position, the system was allowed to relax for 100 ms, which is enough to form molecular junctions between the tip and substrate. The tip was withdrawn by 2

to 5 nm until the low limit of current was reached. The approaching and withdrawing of the tip were done with a rate of 58 nm/s, unless stated otherwise. The current-distance traces were

recorded during the retraction of the tip from the substrate using a digital oscilloscope triggered with a drop current of below 20 µA. These cycles were repeated over several series of 2000 traces

at each set of experimental conditions (with three different bias voltages below 300 mV) to allow a detailed statistical analysis.

Statistical Data Analysis

The raw data collected from the experiment were saved in binary format with the help of a digital oscilloscope. The data were analyzed with home-made software (Lab View 8.6). The data

analysis method is similar to the method proposed by González et. al.,52 but without removal of any tunneling background from the histogram. The histogram is constructed by taking the

logarithm of the entire conductance trace and binning the data using a bin size of 1000. We construct the conductance histogram with 2000 traces that are recorded in the experiment

without any data selection. The conductance histograms were fitted with Gaussian distributions and from the fitting parameters we calculate the most probable conductance value of the

molecule. Every molecule was measured at three different bias voltages (65-300 mV), which

131

Chapter 4

resulted in nearly identical histograms. The conductance values were obtained as the slope of the

linear fit of current (i.e., the maximum of the Gaussian fit of the histogram) versus bias voltage plot with intercept fixed at zero and the values weighed by error. The error in the slope is

presented as error bar for the conductance values.To create the 2D histogram, first the offset of all six channels was nullified by fitting a Gaussian

distribution to a single curve histogram in the noise level. After multiplication of the gain, all the channels were combined to single curves and then we took the logarithm of the entire

conductance trace. The distance axis is obtained from the number of data points, piezo conversion coefficient, and the time settings of the oscilloscope. We generated the 2D histogram

with an automated algorithm which identifies 0.7 (G/Go) of each trace as origin of the elongation axis with binning the data using a bin size of 1000 X 1000 in 2D space.

4.9.3 Theoretical methods53

Calculations of the transport properties of the above molecules were performed using the ab-

initio code SMEAGOL44 which uses a combination of density functional theory (DFT), implemented in the SIESTA code45 and the non-equilibrium Green’s function formalism.

SIESTA uses norm-conserving pseudopotentials to get rid of the core electrons and a linear combination of pseudoatomic orbitals to calculate the single-particle wave functions, which

make it particularly efficient when calculating electronic properties of systems with relatively large numbers of atoms. We also employed the local density approximation (LDA)54 to account

for exchange and correlation effects. SMEAGOL divides the system in three parts: the left lead, the extended molecule, which also includes part of the leads to account for the effect of the

molecule and the surface, and the right electrode. From the DFT Hamiltonian derived from SIESTA, SMEAGOL calculates self-consistently the density matrix, the transmission coefficient

T(E) of electrons from the left to the right lead, and the I-V characteristic.32

132



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11. L. Venkataraman, J.E. Klare, C. Nuckolls, M.S. Hybertsen, M.L. Steigerwald, Nature 2006, 442, 904-907.

12. J.R. Quinn, F.W. Foss, L. Venkataraman, R. Breslow, J. Am. Chem. Soc. 2007, 129, 12376-12377.

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14. D. Vonlanthen, A. Mishchenko, M. Elbing, M. Neuburger, T. Wandlowski, M. Mayor, Angew. Chem. Int. Ed. 2009, 48, 8886-8890.

15. A. Mishchenko, D. Vonlanthen, V. Meded, M. Burkle, C. Li, I.V. Pobelov, A. Bagrets, J.K. Viljas, F. Pauly, F. Evers, M. Mayor, T. Wandlowski, Nano Lett. 2010, 10, 156-163.

16. C. Wang, A.S. Batsanov, M.R. Bryce, S. Martin, R.J. Nichols, S.J. Higgins, V.M. Garcia-Suarez, C.J. Lambert, J. Am. Chem. Soc. 2009, 131, 15647-15654.

17. G. Sedghi, K. Sawada, L.J. Esdaile, M. Hoffmann, H.L. Anderson, D. Bethell, W. Haiss, S.J. Higgins, R.J. Nichols, J. Am. Chem. Soc. 2008, 130, 8582-8583.

18. H. Liu, N. Wang, J. Zhao, Y. Guo, X. Yin, F.Y.C. Boey, H. Zhang, ChemPhysChem 2008, 9, 1416-1424.

19. D. Vonlanthen, J. Rotzler, M. Neuburger, M. Mayor, Eur. J. Org. Chem. 2010, 2010, 120-133.

20. L. Wang, G.M. Rangger, L. Romaner, G. Heimel, T. Bu ko, Z. Ma, Q. Li, Z. Shuai, E.č Zojer, Adv. Funct. Mater. 2009, 19, 3766-3775.

21. D.J. Mowbray, G. Jones, K.S. Thygesen, J. Chem. Phys. 2008, 128, 111103.

22. F. Chen, X. Li, J. Hihath, Z. Huang, N. Tao, J. Am. Chem. Soc. 2006, 128, 15874-15881.

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25. A. Blaszczyk, M. Elbing, M. Mayor, Org. Biomol. Chem. 2004, 2, 2722-2724.

26. M.S. Khan, M.R.A. Al-Mandhary, M.K. Al-Suti, F.R. Al-Battashi, S. Al-Saadi, B. Ahrens, J.K. Bjernemose, M.F. Mahon, P.R. Raithby, M. Younus, N. Chawdhury, A. Köhler, E.A. Marseglia, E. Tedesco, N. Feeder, S.J. Teat, Dalton Trans. 2004, 2377-2385.

27. These dark and insoluble crystals are most likely formed by a combination of cycloadditions and oxidation reactions of 9,10-bis(ethynyl)anthracene. The material does not have considerable conductivity.

28. Measured by Jia Gao and Jochem Smit, University of Groningen.

29. When nitrile anchoring groups are used, then both the HOMO and the LUMO level of the molecules will be lower in energy when compared to thiols. The LUMO is then better aligned with the Fermi energy of gold than the HOMO level is and therefore the charge transport will be influenced by the LUMO level.

30. STM-BJ measurements were performed and analyzed by Veerabhadrarao Kaliginedi and Pavel Moreno García, in the group of prof. Thomas Wandlowski at the Univerity of Bern.

31. C. Li, I. Pobelov, T. Wandlowski, A. Bagrets, A. Arnold, F. Evers, J. Am. Chem. Soc. 2008, 130, 318-326; I.V. Pobelov, Z. Li, T. Wandlowski, J. Am. Chem. Soc. 2008, 130, 16045-16054.

32. For more details see V. Kaliginedi, H. Valkenier, V.M. García-Suárez, P. Moreno-García, W. Hong, P. Buiter, J.L.H. Otten, J.C. Hummelen, C. Lambert, Th. Wandlowski, manuscript in preparation.

33. Z. Huang, F. Chen, P.A. Bennett, N. Tao, J. Am. Chem. Soc. 2007, 129, 13225-13231.


35. S. Creager, C.J. Yu, C. Bamdad, S. O'Connor, T. MacLean, E. Lam, Y. Chong, G.T. Olsen, J. Luo, M. Gozin, J.F. Kayyem, J. Am. Chem. Soc. 1999, 121, 1059-1064.

36. X. Xiao, L.A. Nagahara, A.M. Rawlett, N. Tao, J. Am. Chem. Soc. 2005, 127, 9235-9240.

37. Y. Xing, T. Park, R. Venkatramani, S. Keinan, D.N. Beratan, M.J. Therien, E. Borguet, J. Am. Chem. Soc. 2010, 132, 7946-7956.

38. K. Liu, X. Wang, F. Wang, ACS Nano 2008, 2, 2315-2323.

39. S.C. Veenstra, U. Stalmach, V.V. Krasnikov, G. Hadziioannou, H.T. Jonkman, A. Heeres, G.A. Sawatzky, Appl. Phys. Lett. 2000, 76, 2253.

40. J.R. Quinn, F.W. Foss, L. Venkataraman, M.S. Hybertsen, R. Breslow, J. Am. Chem. Soc. 2007, 129, 6714-6715.

41. M. Tsutsui, M. Taniguchi, T. Kawai, Nano Lett. 2008, 8, 3293-3297.

42. X. Xiao, B. Xu, N.J. Tao, Nano Lett. 2004, 4, 267-271.

43. J.G. Simmons, J. Appl. Phys. 1963, 34, 1793-1803.

44. SMEAGOL is Spin and Molecular Electronics in an Atomically Generated Orbital Landscape; A.R. Rocha, V.M. Garcia-suarez, S.W. Bailey, C.J. Lambert, J. Ferrer, S. Sanvito, Nat. Mater. 2005, 4, 335-339; A.R. Rocha,, S. Bailey, C. Lambert, J. Ferrer, S. Sanvito, Phys. Rev. B 2006, 73, 085414.

134

Chapter 4

45. SIESTA is the Spanish Initiative for Electron Simulations with Thousands of Atoms; J.M. Soler, E. Artacho, J.D. Gale, A. García, J. Junquera, P. Ordejón, D. Sánchez-Portal, J. Phys.: Condens. Matter 2002, 14, 2745-2779.

46. SAiNT is Spectral Adjustment in Nanoscale Transport; D.J. Mowbray, G. Jones, K.S. Thygesen, J. Chem. Phys. 2008, 128, 111103.

47. This requires the gold to be mobile and reorganize to accommodate the displacement of the molecule while reducing its tilt angle.

48. W. Haiss, C. Wang, I. Grace, A.S. Batsanov, D.J. Schiffrin, S.J. Higgins, M.R. Bryce, C.J. Lambert, R.J. Nichols, Nat. Mater. 2006, 5, 995-1002.

49. D. Nilsson, S. Watcharinyanon, M. Eng, L. Li, E. Moons, L.S.O. Johansson, M. Zharnikov, A. Shaporenko, B. Albinsson, J. Martensson, Langmuir 2007, 23, 6170-6181.

50. B. Ren, G. Picardi, B. Pettinger, Rev. Sci. Instrum. 2004, 75, 837-841

51. G. Mészáros, C. Li, I. Pobelov, T. Wandlowski, Nanotechnology 2007, 18, 424004.

52. M.T. González, S. Wu, R. Huber, S.J. van der Molen, C. Schönenberger, M. Calame, Nano Lett. 2006, 6, 2238-2242.

53. Ab-initio calculations were performed by Víctor M. García-Suárez in the group of Colin J. Lambert at Lancaster University.

54. J.P. Perdew, A. Zunger, Phys. Rev. B 1981, 23, 5048.

135


Chapter 4

136

Chapter 5The Influence of the π-Conjugation Pattern on Conductance

In this Chapter we investigate the influence of the pattern of π-conjugation on conductance, using a series of three molecular wires with different conjugation patterns and nearly identical lengths. The anthracene-based molecular wire is linear conjugated, the anthraquinone-based wire is cross-conjugated, and the dihydroanthracene-based wire has a broken conjugation pattern. We have investigated the formation of self-assembled monolayers from these molecular wires and contacted these monolayers with different top-contacts to study their conductance. Conductive Probe Atomic Force Microscopy (CP-AFM) measurements, measurements with a top electrode of eutectic gallium indium (EGaIn), and Mechanically Controllable Break Junction (MCBJ) measurements showed that the conductance of the cross-conjugated wire is about two orders of magnitude lower compared to the linear conjugated wire. The conductance of the cross-conjugated wire is also lower than that of the wire with a broken conjugation pattern, which is attributed to the destructive quantum interference in the transmission function of the cross-conjugated wire.

137

Chapter 5

5.1 IntroductionIn Chapter 2 we have introduced molecular wires in which the conjugation pattern

varies from linear conjugated to cross-conjugated and broken conjugation by

changing the degree of oxidation of the central anthracene-based unit. Having

investigated the growth of high quality self-assembled monolayers from

dithioacetates (Chapter 3) and the influence of length and the HOMO-LUMO gap

on the conductance of linear conjugated molecules (Chapter 4), we will in this

chapter investigate the influence of the conjugation pattern on the conductance, by

studying three rigid dithiolated molecular wires with identical length and different

conjugation patterns: an anthracene-based linear conjugated wire (26AC = 2.6A),

an anthraquinone-based cross-conjugated wire (AQ = 2.1A), and a

dihydroanthracene-based wire with broken π-conjugation (H2AC = 2.7A), as

shown in Figure 5.1. The synthesis and characterization of these molecules is

described in Chapter 2. We will use various junction geometries in this study: CP-

AFM, EGaIn, LAMJ, and MCBJ, as shown schematically in the top row of the

"Matrix Approach" (Figure1.15).

138

Figure 5.1 Overview of the molecular wires that are discussed in this chapter.

The Influence of the π-Conjugation Pattern on Conductance

5.1.1 Conductance of Cross-conjugated Molecular Wires

Cross-conjugation is present in molecules that have “three unsaturated groups, two

of which, although conjugated to a third unsaturated center, are not conjugated to

each other”1 (see Chapter 1.3). The cross-conjugated groups do show electronic

communication,2 although less than linear conjugated molecules.3,4 Therefore,

cross-conjugated molecules are expected to have a lower conductance, as indicated

by the about hundred-fold lower current (at 1 V) that was measured for a molecular

wire with meta-phenylene linkers by Mayor and Weber et al., compared to the same

wire with para-linkers (Figure 5.2).5,6 Similar results were reported for STM Break

Junction experiments on para- vs. meta-substituted benzenedithiols and

benzenediamines,7,8 and also found in computational studies.9,10

However, meta-linked phenylene groups have been proposed as interconnects for

molecular wires.11,12 Alternatively, omniconjugated molecules were designed as

interconnects that provide linear conjugated pathways between all substituents.13

Furthermore, these omniconjugated molecules open the way to perform all 16

Boolean logic operations electrically in relatively compact single molecules, so-

called π-logic.14 This π-logic is based on the difference in conductance between

cross-conjugated and linear conjugated pathways through a molecule. Electrical

transport measurements that confirm this difference are rare. In the experiment of

Mayor and Weber shown in Figure 5.2, in which meta-substituted phenylene

linkers were compared with para-substituted phenylene linkers, not only the

conjugation pattern of the two molecular wires is different, but also their length

and the orientation of the thiol varies.5 Another example is conductance switching

in diarylethene switches,15 as observed in various junctions.1617-1819 The core of these

diarylethene switches is linear conjugated in the closed state and cross-conjugated

in the open state (Figure 2.2). Indeed, the closed (linear conjugated) state is

measured to have a higher conductance that the open (cross-conjugated) state.

However, not only the conjugation pattern, but also the geometry of these

139

Figure 5.2 Mayor et al. found higher currents for the linear conjugated para-substituted molecular wire (left) than for the cross-conjugated meta-substituted one (right).5

Chapter 5

molecules and the framework of -bondsσ changes dramatically upon switching.

For that reason, we have designed a cross-conjugated anthraquinone-based redox

switch (AQ), which becomes linear conjugated upon reduction to its hydroquinone

state (Figure 2.1).20 The great advantage of this switch is that the cross-conjugated

and linear conjugated state have an identical length and geometry and only differ

in their electronic properties. This results in a low reorganization energy, which

opens opportunities for high frequency switching.

5.1.2 Quantum Interference Effects

Very recently, the conductance of this redox switch was studied by several

computational methods and the transmission curve of the cross-conjugated

anthraquinone wire showed a quantum interference effect:21 at certain energy, the

transmission probability of the electrons drops sharply due to destructive

interference.22 For our anthraquinone-based molecular wire, bound to two gold

electrodes, this dip in the transmission curve was found at the Fermi energy

(Figure 5.3). No quantum interference effect was found for the hydroquinone state

of the molecule.21 The quantum interference effect for the anthraquinone-based

wire originates from the cross-conjugated nature of the pathway through the

molecule, which can be concluded from a computational study in which the

topology of the molecular wire was varied.23 Though quantum interference effects

are generally found for cross-conjugated pathways,4,2425

-26 they are not limited to the

class of cross-conjugated molecules only and have for instance been calculated for

linear conjugated molecules with nitro-substituents.27,28 Quantum interference

effects can be tuned by molecular structure and gating (in a three-terminal device),

opening the way to functional molecular devices as transistors29,30 and rectifiers.31

Quantum interference effects result in very small conductances at low bias

140

Figure 5.3 Transmission curves from DFT-based transport calculations through our cross-conjugated anthraquinone-based molecular wire (AQ) and the corresponding hydroquinone wire (HQ), adapted from ref. 21.


voltages. According to calculations based on Hückel methods (which only consider

the π-system), the conductance of cross-conjugated molecular wires at low bias

voltages could be even lower than that of wires that contain saturated (sp3-

hybridized) carbon atoms. Though at larger voltages (~1 V), the conductance of

cross-conjugated molecules increases rapidly, which causes the I-V curves of the

cross-conjugated wire and the wire with broken conjugation to cross.4 However,

when transport through -bonds σ is taken into account in DFT-based calculations,

then the conductance of (short) cross-conjugated molecules is at least the

conductance of molecules with broken conjugation, since at energies where the

transmission through the π-system approaches zero, the -system will provide theσ

main channel for the transmission.10,24

No direct experimental evidence for quantum interference effects in charge

transport through molecular junctions with cross-conjugated molecular wires has

been reported until now. Recent charge transfer experiments show slower transfer

through a cross-conjugated bridge compared to a linear conjugated bridge.32

5.2 Formation of Self-Assembled Monolayers

5.2.1 Deprotection by Et3N

In Chapter 3 we have described how high quality Self-Assembled Monolayers

(SAMs) from conjugated dithioacetates can be grown. It is important to generate a

small amount of monothiolate anion in a solution of bisacetyl-protected dithiols,

which was achieved by addition of around ten volume percent of triethylamine

(Et3N) to a 0.5 mM solution of the acetyl protected molecular wires in THF. We

have applied this optimized procedure for the growth of SAMs from molecular

wires 26AC, AQ, and H2AC. We found that the solubility of 26AC and AQ is

lower than that of OPE3 and only 0.3 mM solutions in THF could be obtained. A

precipitate was observed in these solutions about two days after the addition of

Et3N, which gave tailing at the low-energy end of the UV-Vis spectra. Since the

solubility of these molecular wires is higher in chloroform, we have made 0.5 mM

solutions in chloroform, with 10% (v/v) Et3N added. In the UV-Vis spectra of

these solutions we did not observe any tailing or other changes, compared to the

spectra without Et3N.

141

Chapter 5

We immersed samples of gold on mica upside down in 0.5 mM solutions of 26AC,

AQ, H2AC, and OPE3 in chloroform with 10-13% Et3N for two days and

analyzed the resulting SAMs by ellipsometry (see Table 5.1). The length of all

anthracene-based compounds is 24 Å. We would therefore expect their SAMs to be

slightly thicker than that of OPE3, which has a length of 20 Å. Only for AQ we

found a SAM that was slightly thicker than OPE3, as predicted. For H2AC we

found a thinner SAM, which is most likely due to the nod (max. 30°) in the

backbone of H2AC, caused by the sp3 hybridized carbon atoms, which could result

in a different packing to optimize the π-π stacking. For the SAM of 26AC we

measured a thickness that is larger than expected for a monolayer. This could

originate from the assumptions that we make in the fitting of our ellipsometry

measurements (see Chapter 3.8.3); we assume that the index of refraction (n) is

1.55 for all π-conjugated thiols and that the SAMs do not absorb between 300-800

nm. As depicted in Figure 2.7, all molecular wires do absorb above 300 nm. Even

though these assumptions did not give any problems for the OPE molecules

discussed in Chapter 3, 26AC shows transitions around 400 nm and could

therefore obfuscate the ellipsometry measurements. The high reproducibility of the

measured large thickness indicates that this is not due to the formation of

multilayers.

Table 5.1: Molecular Length the Thicknesses found by ellipsometry and XPS.

Molecular Wire

Length a

(Å)Ellipsometry

(Å)XPS

method A (Å)XPS

method B (Å)

26AC 24.20 28.6 24.1 27.1

AQ 24.25 21.7 20.1 26.9

H2AC 24.06 19.1 18.3 20.1

OPE3 19.83 19.7 17.5 17.8

a. The distance from S- to S-atom as calculated with HyperchemTM Release 7.52 for Windows Molecular Modeling Systems. Structures were optimized using the AM1-RHF method. We used methyl-substituted thiols in the calculations.

We performed X-ray Photoelectron Spectroscopy (XPS) measurements to

determine the thickness and composition of the SAMs. We determined the

thicknesses of the SAMs from our XPS measurements by two different methods:

A) from the ratio between the carbon and the gold signals33 and B) from the

attenuation of the gold signal34 (details are given in Chapter 3.8.4). In Chapter 3 we

142


found method A to be more reliable compared to method B, since method B is

more sensitive to experimental errors (as alignment of the sample and intensity of

the X-ray beam). However, the equation that we used to determine the thickness by

method A has been derived for hydrocarbon compounds and does not take into

account heteroatoms as oxygen and sulfur. The error caused by not considering

unbound sulfur is the same in all four SAMs. The thickness of the SAM of AQ is

further underestimated, because of the oxygen atoms at the anthraquinone core,

which can explain the relatively low value that we found for the thickness of AQ

by method A, where the thicknesses of AQ is nearly identical to the thickness of

26AC when we use method B. Even though different methods gave different values

for the thicknesses of the SAMs from our anthracene-based molecular wires, the

trend is clear: the SAM of 26AC has the largest thickness (25 Å), directly followed

by that of AQ (24 Å), while the SAM of H2AC has a similar thickness as that of

OPE3 (19 Å).35

A more detailed analysis of the different peaks in the XPS spectra (Figure 5.4 and

Table 5.2) gave information about the composition of the three SAMs of the

anthracene-based molecular wires. For all three SAMs we found two sulfur signals,

of which the smallest (162 eV) corresponds to sulfur bound to gold and the larger

one (164 eV) to either free thiol or acetyl protected thiol (we will refer to this signal

as “unbound” sulfur). As for the OPEs (Chapter 3.4), we did not find any

indications of oxidized sulfur (S=O, 168 eV). Furthermore, we found an intensity

per carbon atom that approaches the average of the intensities of bound and

unbound sulfur signals. These are clear indications of a SAM comprised of

molecular wires that are standing instead of laying flat on the gold surface.

Table 5.2 Composition of the SAMs: X-ray Photoelectron Spectroscopy Measurements

Molecular Wire

Integrated Intensities a Normalized Intensities

C1sper C-atom b

Au4f

84 eV

C1sCxHy

283-287 eV

C1sC=O288 eV

S2p S-Au162 eV

S2pS-R

164 eV

O1s

532 eV

26AC 7515 1343 39 19 84 57 43

AQ 7564 1017 73 18 55 102 36

H2AC 9919 1228 0 24 55 12 41

a. These areas are divided by the sensitivity factor: 1 for C1s, 1.79 for S2p, 2.49 for O1s, and 1.68 for N1s.b. The total area of the CxHy C1s signal is divided by the number of C-atoms in the core of the molecular wire.

We correct for the presence of carbonyl C-atoms.

143

Chapter 5

In the C1s spectrum of AQ we found a relatively large peak at 288 eV, which is

attributed to the carbonyl carbon atoms of the anthraquinone core. We found a

smaller signal at 288 eV for the SAM of 26AC, which we attribute to acetyl

protecting groups at the unbound sulfur atom. On comparing its area to that of the

unbound sulfur signal (164 eV), we can conclude that half of the sulfur atoms that

are not bound to gold bear an acetyl protecting group, in good agreement with our

results for OPE3 (see Chapter 3.4). In contrast, we have not detected any

remaining acetyl groups in the SAM of H2AC, while we cannot draw any

conclusions on that for the SAM of AQ. We have not observed any signals from

nitrogen or chlorine atoms, indicating that no solvent or base is incorporated in the

SAM.36

144

Figure 5.4 C1s (a, d, g), S2p (b, e, h), and O1s (c , f, i) XPS signals for SAMs from 26AC (a-c), AQ (d-f), and H2AC (g-i). Fits are shown as lines.


5.2.2 Deprotection by Bu4NOH

We have investigated the deprotection of the anthracene-based molecular wires by

tetrabutylammonium hydroxide (Bu4NOH, see Chapter 3.3.2), which is commonly

used to apply bis acetylprotected dithiols in STM break junctions. However, in

contrast to the molecular wires that were studied by this approach in Chapter 4,

anthraquinone and dihydroanthracene units are more reactive than acene units and

could react with the hydroxide. For that reason, we compared the changes in UV-

Vis absorption spectra of solutions of acetyl protected dithiols (suffix A) AQ and

H2AC to those of tert-butyl protected dithiols (suffix B) upon addition of

Bu4NOH.

Figure 5.5 a and c show the UV-Vis absorption spectra of a solution of diSAc-

anthraquinone-wire AQ (2.1A) and its tert-butyl protected analogue (2.1B) in THF.

The color of the solution of 2.1B changed from yellow to green upon addition of

Bu4NOH, as indicated by the changes in its UV-Vis spectrum. While tert-butyl

thioethers are rather inert to strong bases and nucleophiles, the hydroxide anion

could easily attack the carbonyl groups of the anthraquinone unit. The obtained

spectrum from 2.1B with Bu4NOH is similar to that shown in Figure 2.10, in

which 2.1B was reduced electrochemically to the hydroquinone dianion, indicating

145

Figure 5.5 UV-Vis absorption spectra of 0.15 mM solutions of 2.1A=AQ (a) and 2.1B (b), and 0.30 mM solutions of 2.7A=H2AC (c) and 2.7B and 2.6A=26AC (d) in THF, with and without Bu4NOH, showing not only the conversion of thioacetate into free thiolate, but also reactions of hydroxide with the anthraquinone and dihydroanthracene cores.

Chapter 5

that also under the conditions used here the anthraquinone is reduced to the

hydroquinone dianion.

In Chapter 3 we observed a shift of 100-120 nm in the UV-Vis absorption spectrum

of OPEs upon the reaction of a conjugated thioacetate with Bu4NOH to its

thiolate anion. The UV-Vis spectra of AQ (2.1A) did not only show this new

absorption with a redshift of about 100 nm, but also a new absorption band

around 650 nm appearing upon addition of Bu4NOH. This additional absorption

is similar to that found for 2.1B upon addition of Bu4NOH and it is already

observed upon addition of 2 eq. Bu4NOH. This indicates that the reaction of

Bu4NOH with the thioacetates of AQ is not selective and competes with the

reaction with the anthraquinone units, or that the formed thiolate anions give rise

to a similar reduction of the anthraquinone unit as Bu4NOH does.

Figure 5.5 b and d show the UV-Vis absorption spectra of solutions of diSAc-

dihydroanthracene-wire H2AC (2.7A) and its tert-butyl protected analogue (2.7B)

in THF. Upon addition of Bu4NOH to H2AC we observed a change of the color

from colorless to orange and found a new absorption around 400 nm that grows

when increasing the amount of Bu4NOH from a halve to five equivalents. We

attribute this absorption to the formation of the thiolate anion. However, after

having measured these spectra, we observed that the solution in the cuvette (with

Teflon stopper and sealed with parafilm) slowly turned red, starting from the

gas/liquid interface. After 30 minutes we measured the UV-Vis absorption

spectrum again and found a completely different spectrum, which is identical to

that of a solution of diSAc-2,6-anthracene-wire 26AC (2.6A) with over four

equivalents of Bu4NOH added (Figure 5.5d), which shows the common 100 nm

redshift due to the formation of thiolate anion. The solutions of H2AC with

Bu4NOH in the glove box did not change color upon time. This teaches us that

Bu4NOH with a trace amount of oxygen converts the dihydroanthracene unit of

H2AC into an anthracene unit as present in 26AC. The thiolate anions could also

play a role in this reaction. Addition of one equivalent of Bu4NOH to the tert-butyl

protected dihydroanthracene wire also gave rise to change of the color (from

colorless to blue) as shown in its UV-Vis spectrum, showing that Bu4NOH indeed

reacts with the dihydroanthracene core. From these UV-Vis studies on AQ and

H2AC we can conclude that Bu4NOH is not a suitable deprotecting agent to

facilitate the formation of SAMs from these molecules.

146


5.3 Conductance Measurements using Conductive Probe Atomic Force Microscopy37

We have grown SAMs of molecular wires 26AC, AQ, and H2AC on gold coated

silicon samples (using Et3N as deprotecting agent, Section 5.2.1) and contacted

these SAMs with a gold coated contact mode AFM tip (Figure 5.6a). The current

through these junctions was measured as function of the bias voltage and the

conductance was obtained from the slope of the linear regime of the I-V curves at

low bias (-100 mV to 100 mV). From the measurements of about 200-1000 I-V

curves per spot and 3-6 spots per sample, we obtained the conductance histograms

shown in Figure 5.6b. Since the geometry of the contact and thus the number of

molecules contacted varies from measurement to measurement, a distribution of

conductance values is obtained.38

Linear conjugated 26AC clearly shows the largest conductance. The Gaussian fit

of the histogram is centered around 10-2.5 G0 (221 nS). The conductance of the

SAM of 26AC is lower than the conductance found for a SAM of OPE3 (841 nS)

and larger than for a SAM of OPE4 (63 nS, see Chapter 7), in agreement with the

single molecule conductance studies discussed in Chapter 4.

We measured significantly lower conductance values for cross-conjugated wire AQ

(10-4.1 G0, 7 nS) than for linear conjugated 26AC. This difference of a factor 32

between the centers of the histograms reflects the reduced electronic coupling

caused by the cross-conjugation. These measurements unambiguously show the

147

Figure 5.6 a. Schematic of the molecular wires in the CP-AFM junction. b. Histograms from CP-AFM measurements on 26AC (blue), AQ (red), and H2AC (black) showing the 32 times larger conductance of linear conjugated 26AC compared to cross-conjugated AQ (Leiden, note 37)

Chapter 5

influence of π-conjugation on conductance, supporting the assumptions made

when developing the π-logic concept (Chapter 1.3).

Reference compound H2AC gave conductance values around 10-3.4 G0 (32 nS), in

between those of AQ and 26AC. This result is counterintuitive, since the π-

conjugation pattern in H2AC is completely broken (which is reflected by its UV-

Vis absorption, see Chapter 2.3 and Figure 5.5), whereas the π-conjugation in AQ

and 26AC extents over the full carbon framework, resulting in identical optical

HOMO-LUMO gaps for these two molecules. For that reason, we had expected

the conductance of H2AC to be below that of AQ (and 26AC). However, when we

look at the HOMO levels (Chapter 2.5) of this series of molecules with identical

length and use the simple model for tunneling through a rectangular barrier (see

Section 4.5.2) to predict the trends in the conductance values of this series, we

would indeed expect AQ to have the lowest conductance, 26AC to have the largest

conductance, and H2AC to be in between. However, according to this model, the

difference between AQ and 26AC would be no more than a factor four. Thus, the

relatively low HOMO level of AQ cannot account for its much lower conductance

and the simple model for tunneling through a rectangular barrier is not sufficient to

explain the trends shown in Figure 5.6. For that reason, DFT-based transport

calculations were performed.

5.4 DFT-NEGF Transport Calculations39

The transmission functions of molecular wires 26AC, AQ, and H2AC were

calculated by Troels Markussen and Kristian Thygesen, Technical University of

Denmark, using Density Functional Theory (DFT) in combination with non-

equilibrium Green's function (NEGF)4041

-42 (see Figure 5.7). Both thiolate anchoring

groups were bound to the gold surface of the electrodes at a bridge site slightly

displaced towards the hollow site, which was found to be energetically most

favorable. The transmission functions approach unity at energy values that

correspond to the energies of the molecular orbitals, though standard DFT

calculations are known to underestimate the HOMO-LUMO gap. For linear

conjugated molecular wire 26AC we found a transmission maximum that

corresponds to transport through the HOMO level around -0.6 eV, whereas the

LUMO related maximum is located around 1.3 eV. Since the maximum related to

148


the HOMO is found closer to the Fermi energy, this calculation suggests that the

HOMO is the main orbital to contribute to the charge transport through molecular

wire 26AC. We found a maximum in the transmission through cross-conjugated

molecular wire AQ at 0.9 eV. This LUMO-related maximum is located closer to

the Fermi energy than the LUMO-related maximum of wire 26AC, in agreement

with strong electron accepting character of the anthraquinone unit, caused by the

electron withdrawing carbonyl groups, resulting in frontier orbitals that are lower

in energy than those of wire 26AC. The transmission maxima calculated for wire

H2AC (-0.7 eV and 2.0 eV) are located much further from the Fermi energy than

for the other two wires, all in good agreement with its broken conjugation pattern

and with the wider HOMO-LUMO gap that we found for this molecule in the

optical experiments.

Linear conjugated 26AC clearly has the largest transmission around the Fermi

energy of the gold electrodes, in good agreement with the largest conductance

values found for 26AC in the CP-AFM experiments. The transmission function of

cross-conjugated anthraquinone wire AQ shows a destructive quantum

interference at 0.25 eV (Section 5.1.2). Due to this interference it crosses the

transmission function of dihydroanthracene wire H2AC, of which the π-conjugation is broken by sp3-hybridized methylene groups in the center of the

molecule. The exact position of the quantum interference dip depends on

parameters such as the basis set, binding site, and structure used in the

calculations. This quantum interference effect causes the transmission of AQ at the

Fermi energy of the electrodes (and thus the conductance) to be smaller than that

of H2AC. The order of this difference cannot be calculated exactly, due to the

relatively large uncertainty in the position of the dip with respect to the Fermi

149

Figure 5.7 Transmission functions of AQ (red), 26AC (blue), and H2AC (black). (Denmark, note 39)

Chapter 5

energy. Quantum interference convincingly explains the lower conductance of AQ

compared to H2AC.

5.5 Conductance Measurements in EGaIn Junctions43

SAMs of AQ, 26AC, and H2AC on gold on mica were contacted with tips of the

eutectic alloy of gallium (75%) and indium (25%) (EGaIn) as described in Section

1.4.4 (inset in Figure 5.8a).44 The current was measured as function of the applied

bias between the EGaIn tip and the (grounded) gold surface of the sample. The

contact area was estimated from the image of a high magnification camera and

used to calculate the current densities. Around 200 I-V curves were recorded for

each SAM and current density histograms were obtained for each voltage (Figure

5.8b). The centers of the Gaussian fits45 of these histograms are plotted in Figure

5.8a.46

In this setup, the conductance of linear conjugated 26AC is significantly larger

than the conductance of AQ (cross-conjugated) and of H2AC (broken

150

Figure 5.8 a. Mean values of the current densities from Gaussians fits of the current density histograms versus the bias voltage, obtained for EGaIn contacted SAMs of AQ, 26AC, and H2AC on gold on mica. b. Histograms of the current densities measured through EGaIn contacted SAMs of 26AC (blue, 782 I-V curves), H2AC (black, 268 I-V curves), and AQ (red, 232 I-V curves) on gold on mica at 100 mV bias voltage. (note 43)


conjugation). The current densities as obtained from Gaussian fits were slightly

larger for H2AC than for AQ. However, when comparing the distributions of the

current densities measured for these SAMs, we find a similar spread of the current

densities of AQ and H2AC. The histograms of 26AC clearly depict a larger

population at higher current densities, compared to AQ and H2AC.

A main cause of the spread in the data is the roughness of the annealed mica

surface, which is known to have large flat terraces of gold (111), but also very steep

trenches, making the overall roughness relatively large.47 Samples for EGaIn

measurements are generally prepared by template stripping a metal film from a

Si/SiO2 surface,44,48,49 by which ultraflat polycrystalline surfaces are obtained,

compared to evaporated metal layers.50 The use of these ultraflat metal surfaces

significantly reduces the error in charge transport measurements on SAMs.51

However, the technique of template stripping (and especially the commonly used

optical adhesive) is not compatible with organic solvents as chloroform and THF,

which are required to dissolve our rigid π-conjugated dithioacetates. Other

parameters influencing the spread in the data and influencing the reproducibility

are for instance the shape of the tip, the gallium oxide layer, temperature, and

humidity.52,53

A subtle asymmetry is visible in the J-V curves in Figure 5.8a, which reflects the

asymmetry in the contact geometry: the molecules are bound with one thiolate

anchoring group to the gold substrate (with a work function of around -5.0 eV),

while the other thiolate (or thioacetate) group is in contact with the EGaIn tip

(work function around -4.1 eV).43 Such an asymmetry was not found in the CP-

AFM measurements.

The difference between AQ and H2AC is not significant in these EGaIn

measurements, which could be caused by the different Fermi energy of the

Ga2O3/GaIn electrode compared to the gold coated AFM tip, which influences the

position of the interference minimum in the transmission function (and thus the

position where the transmissions of AQ and 26AC cross). Strikingly consistent

with the CP-AFM measurements, linear conjugated 26AC gave one to two orders

of magnitude higher current densities than AQ and H2AC.

151

Chapter 5

5.6 Conductance Measurements in Large Area Molecular Junctions54

Large Area Molecular Junctions (LAMJ) devices55 were made with molecular

wires 26AC, AQ, H2AC, and OPE3. These devices were fabricated on 4-inch

wafers and consist of a gold bottom contact on which a SAM is grown in a

lithographically defined pore (5-100 m in diameter). The top contact is made byμ

spin coating the conducting polymer PEDOT:PSS (~90 nm) and subsequent

evaporation of gold (see inset Figure 5.9a, details are reported in Section 5.9.4).

We measured the currents through these devices as function of the voltage and

found a good scaling of the currents with the device areas. The averaged current

densities are plotted in Figure 5.9a and the distributions of the current densities at

100 mV are shown in Figure 5.9b.

In these LAMJ experiments we found the current densities (or conductance) of

broken conjugated H2AC to be a factor six lower than those of linear conjugated

26AC. This difference is less pronounced than in the CP-AFM and EGaIn

junction, but the trend is the same. However, cross-conjugated AQ gave current

densities in between those of 26AC and H2AC. We attribute this difference to the

special nature of the top contact in LAMJs: the PEDOT:PSS has a dominant role

152

Figure 5.9 a. I-V characteristics of Large Area Molecular Junctions with 26AC, AQ, and H2AC. b. Histograms of the distribution of current densities at 100 mV. (note 54)


on the charge transport (see Chapter 7),56 which is not yet understood. For that

reason, it is hard to predict the influence of quantum interference on the

conductance of LAMJs containing AQ. It could be that the minimum in the

transmission curve is shifted away from the Fermi energy, resulting in a larger

currents for AQ than for H2AC.46 Alternatively, quantum interference effects could

be absent in LAMJs, resulting in a trend that follows the relative degree of

conjugation of the three molecular wires.

5.7 Single Molecule Conductance Measurements57,58

In Section 5.2.2 we have described the problems that arose when deprotecting

molecular wires AQ and H2AC with the strong base and strong nucleophile

Bu4NOH, which was used to deprotect the conjugated dithioacetates for the

Scanning Tunneling Microscopy Break Junction (STM-BJ) experiments described

in Chapter 4. For this reason, the conductance of AQ and H2AC was not studied

by STM-BJ. In the single molecule conductance studies presented in this Section

no deprotecting agent was used to hydrolyze the thioacetate groups, since

thioacetate groups can bind to gold and spontaneously form thiolate-gold bonds

(see Chapter 3). The lower coverages obtained without deprotection do not hinder

the single molecule studies in Mechanically Controllable Break Junctions

(MCBJs).

Wenjing Hong measured conductance histograms of 26AC, AQ, and H2AC by

repeatedly opening and closing of notched gold wire-based MCBJs in the presence

of solutions of the molecular wires, at the University of Bern (Figure 5.10). The

blank measurement with solvents only shows a conductance peak at 10 -8.8 G0,

which is attributed to the noise level of the setup. The conductance histograms of

the molecular wires all show clear peaks at 1 G0 (single gold atom contact) and a

noise peak below 10-8 G0. Apart from these peaks, the histogram of 26AC shows a

very clear peak at 10-4.6 G0 (1.95 nS), which is close to the conductance value of 3.6

nS as determined by STM-BJ (Chapter 4, wire 4.7). The less pronounced peak

around 10-7 G0 could be caused by an alternative binding geometry of the

molecular wires (see Chapter 4.7) or by π-π stacking of molecules (see Section

7.2.3). The conductance histogram of AQ shows a peak at 10-7.0 G0 (0.0078 nS),

153

Chapter 5

indicating that the most probable single molecule conductance value of this cross-

conjugated molecular wire is 250 times lower than that of linear conjugated 26AC.

The histogram of H2AC shows a conductance peak at 10-6.3 G0 (0.039 nS)59, which

is fifty times lower than 26AC, though five times larger than AQ. This trend is the

same as that found in the CP-AFM and EGaIn experiments, although the

differences between the conductance values are larger.

The conductance of molecular wires AQ and 26AC was investigated in

lithographically defined MCBJs60 (operated in vacuum and at room temperature)

by Mickael Perrin and Diana Duli at Delft University. The ć 2D histograms of the

opening conductance-distance traces are depicted Figure 5.11 and show plateau-

like features for both molecules. The plateaus in the 2D histogram measured for

26AC (Figure 5.11a) are mainly found between 10-4 and 10-5 G0, resulting in a peak

154

Figure 5.10 Conductance histograms of 26AC (blue), AQ (red), and H2AC (black) measured in notched gold-wire MCBJ experiments in a liquid cell at room temperature (450 traces each). The conductance histogram obtained in decane/THF (4:1) in the absence of molecules wires is shown for comparison (green, 200 traces). The main conductance peaks are indicated by their values in log (G/G0). (Bern, note 57)


around 2 10· -5 G0 (1.6 nS) in the conductance histogram, in good agreement with

the values found in the STM-BJ and MCBJ experiments at Bern. The plateaus

observed in the 2D histograms measured for cross-conjugated AQ are located

between 10-5 and 10-6 G0, which is at the low current limit of the setup (as indicated

by the noise in the histograms). Although a clear conductance value cannot be

determined for AQ, these measurements support the conclusion that the linear

conjugated anthracene wire (26AC) has a higher conductance than the cross-

conjugated anthraquinone wire (AQ). More detailed investigations at low

temperatures are ongoing at the moment of writing this thesis.

5.8 ConclusionsWe have investigated the influence of the π-conjugation pattern on conductance by

measuring the electrical transport properties of three molecules with similar length

and different conjugation patterns in various junctions. We were able to grow

SAMs of the three molecular wires, following the methodology described in

Chapter 3.

Electrical measurements through these SAMs using a conductive probe AFM tip

or an EGaIn tip as top contact showed that linear conjugated anthracene-based

wires had an almost two orders of magnitude higher conductance than the cross-

conjugated anthraquinone-based wires. The dihydroanthracene-based wire with a

155

Figure 5.11 Normalized 2D histograms (left panel, logarithmic color scale) and conductance histograms (right panel) of the conductance-distance traces from MCBJ experiments on a. 26ACQ and b. AQ. The junctions were closed to a conductance of 10 G0 and opened with a speed of 1.5 nm/s in vacuum at a bias voltage of 150 mV. (Delft, note 58)

Chapter 5

broken conjugation pattern had a slightly higher conductance than the cross-

conjugated anthraquinone-based wire. This is best explained by DFT-based

transport calculations, which revealed a destructive quantum interference for the

cross-conjugated anthraquinone wire, resulting in a very low transmission close to

the Fermi energy of the electrodes. This quantum interference effect causes the

transmission functions of the cross-conjugated and broken-conjugated wires to

cross, resulting in a lower conductance of the cross-conjugated anthraquinone-wire

compared to the broken-conjugated dihydroanthracene wire. This order could be

altered by a small change in the Fermi energy of the electrodes. This might explain

why in Large Area Molecular Junctions the anthraquinone-based wire had a larger

conductance than the dihydroanthracene wire, though still lower than the linear

conjugated anthracene-wire. However, the presence of PEDOT:PSS makes these

junctions complicated to understand and quantum interference could be absent.

The trends that were found in CP-AFM junctions and EGaIn junctions were

confirmed by single molecule conductance measurements in break junctions: the

linear conjugated anthracene wire has a much higher conductance than the cross-

conjugated anthraquinone wire, whereas the broken-conjugated wire has a slightly

higher conductance than the cross-conjugated wire.

Although we have found different conductances for the cross-conjugated

anthraquinone-wire and the linear conjugated anthracene wire independently in

this chapter, we have not yet been able to measure in situ conductance switching

upon (electro)chemical reduction and subsequent oxidation of the anthraquinone

wire as described in Chapter 2 and depicted in Figure 5.3, though various efforts

towards this aim are ongoing.

The clearly lower conductance found for the cross-conjugated wire than for the

linear conjugated wire provides experimental support for one of the fundamental

assumptions made when developing the π-logic concept (Chapter 1.3). This study

constitutes the first direct comparison of molecular conductance experiments on a

set of fundamentally different π-conjugated systems present in three molecules of

nearly identical shape and length.

156



5.9.1 Preparation and analysis of the solutions and SAMsDry chloroform was used (Aldrich anhydrous, ≥99%, contains amylenes as stabilizer). Triethylamine (Et3N) was purchased from Fisher (HPLC grade) and degassed.

Tetrabutylammonium hydroxide 30-hydrate (Bu4NOH) was purchased from Sigma-Aldrich and stored under dry nitrogen.

All solutions and SAMs were prepared inside a glovebox filled with nitrogen (<5 ppm O2). SAMs were grown in two nights (40-44 h) from 0.5 mM solutions in chloroform, with 10% (v/v)

Et3N added, unless stated otherwise. The solutions of AQ and 26AC were stirred and heated till 50°C, and -if particles were observed by eye- filtered through a 1 m PTFE syringe filter byμ

gravity. We used freshly prepared samples of 150 nm gold on mica for the ellipsometry, XPS, and EGaIn studies and freshly prepared samples of 2-5 nm chromium and 200 nm gold thermally

deposited on a silicon wafer for the CP-AFM studies. After two days, samples were taken from solution and immersed three times in vials with clean THF, after which the samples were dried in

the glovebox or with a nitrogen pistol.UV-Vis absorption spectra of the solutions were measured on a Perkin Elmer Lambda 900

Spectrometer in a 1 mm quartz cuvette with Teflon stopper.Ellipsometry measurements were performed using a V-Vase from J. A. Woollam Co., Inc. in air.

Measurements were acquired from 300-800 nm with an interval of 10 nm at 65, 70, and 75º angle of incidence. For every set of experiments a fresh gold-on-mica sample was measured at

three or four different spots. The data from these measurements were merged and the optical constants were fitted. For every SAM three spots were measured and the thickness of a cauchy

layer (n=1.55, k=0 at all ) on top of the gold layer was fitted and averaged over the three spots.λXPS measurements were performed on a X-PROBE Surface Science Laboratories photoelectron

spectrometer with a Al K X-ray source (1486.6 eV) and a takeoff angle of 37º. We accumulatedα 20 scans for S2p, 10 for C1s, 10 for O1s, 15 for N1s, and 5 for Au4f. All reported data are

averaged over three different spots per sample. See Chapter 3.8.4 for details on the fitting of the data with WinSpec61 and calculation methods for the thickness.

5.9.2 CP-AFM Measurements37

The measurements were performed on a Multimode 8 atomic force microscope base using a

Nanoscope III controller. The AFM cantilevers (Veeco NP-10 chips, B cantilever, 0.12 N/m and 14-26 kHz) were sputtered with MoGe (4 nm) as an attachment layer prior to the Au layer (80

nm). Before every measurement the tips were cleaned by an oxygen plasma. The samples were prepared by growing SAMs on Au-coated Si/SiO2 substrates as explained in Section 5.9.1.

Subsequently, the sample was electronically connected to the scanner with silver paint and the scanner was connected to the data acquisition card via the AFM breakout box. Using a modified

tip holder, the (grounded) cantilever was connected to the I/V converter (Femto DLPCA-200). The AFM was operated in contact mode with the scanning range set to 0 nm in order to contact

continuously the same area of the SAM. To insure a soft contact with the molecules, a force of

157

Chapter 5

approximately 2 nN was applied and maintained constantly using feed-back on the deflection of

the cantilever. Once the molecules were contacted, the current sensing was switched on as it is externally driven

by Labview. A bias voltage was applied to the tip-sample junction and swept from 0 V to 1.2 V to -1.2 V and back to 0 V typically. Simultaneously the current was recorded at a sampling rate of

10 kHz. We recorded 200 to 1000 of such I-V curves for each of the three to six spots per sample. For each molecule we computed all the measured I-V curves into a linearly averaged I-V curve.

The conductance histograms were build up from low bias (100 mV) conductances of individual I-V curves. Those conductances were logarithmically binned and plotted linearly.

5.9.3 EGaIn Junctions52

The EGaIn setup was composed of an EGaIn filled 10 L syringe with a flat needle, a CCDμ

camera with a variable-zoom telescopic lens, a piezo-crystal for high precision motion control of the syringe, and a subfemto-Amperometer with external current amplifier (Keithley 6430). The

EGaIn tips were formed by placing a big drop of EGaIn on a surface and subsequent withdrawal the syringe with the piezo. The speed and the step voltages applied to the syringes determined the

shape of the EGaIn tip. The sample and the amperometer were grounded and a voltage was applied on the syringe filled with EGaIn. The sample was approached with the EGaIn tip first

manually (no contact, 1-5 pA at 100 mV bias voltage), then with the piezo until the current started to increase. Five I-V traces were measured per spot, from 0 to 0.4 to -0.4 to 0 V, at ~20

spots per sample.

5.9.4 Large-Area Molecular Junctions54

A 4-inch silicon wafer with a 500 nm thermally grown oxide was passivated using hexamethyldisilazane (HMDS). A 1 nm layer of chromium was thermally evaporated through a

shadow mask, followed by 60 nm of gold. The rms roughness of the bottom contact was about 0.7 nm over an area of 0.25 mμ 2. The two terminal junctions were photolithographically defined

in an insulating matrix of photoresist, ma-N 1410 (Micro Resist Technology GmbH). The negative photoresist was spin cast on the wafer resulting in a layer of 570 nm. After a pre-bake

step to remove any remaining solvents, the layer was exposed to UV light with a Karl Süss MA1006 mask aligner, to define the vertical interconnects, ranging from 5 m to 100 m inμ μ

diameter. After development, the film was hard-baked at 200°C for at least 1 hour to render the photoresist insoluble in organic solvents. The wafer was subsequently cut in 4 pieces using a

diamond tip pen. This allowed the simultaneous processing of different SAMs on a single wafer, thereby eliminating processing variations that can affect device performance. A last step before

self-assembly was cleaning of the bottom gold contacts with a PDC plasma cleaner (Harrick plasma) to remove any photoresist residuals.

The self-assembled monolayers were formed from 0.5 mM solutions in chloroform with 10% Et3N in 44 hours in a glove box (wafer pieces were immersed upside down in the solutions).

After that, the wafer pieces were thoroughly rinsed with chloroform in ambient. Subsequently, the interlayer of PEDOT:PSS, a water-based suspension of poly(3,4-ethylenedioxythiophene)

and poly(4-styrenesulfonic acid), was spin cast. PEDOT:PSS acts as a highly conductive buffer layer that protects the SAM during subsequent evaporation of the top gold contact. The

158


commercially available PEDOT:PSS AGFA® ICP new type, filtered over a 5 m Whatmanμ ®

glass filter, was used. The PEDOT:PSS solution was spin cast, resulting in a layer thickness of about 90 nm. The wafer was then immediately transferred to a vacuum oven for at least 1 hour to

dry the film. To facilitate contacting the top electrode, approximately 100 nm of gold was evaporated through a shadow mask. This gold layer, apart from ensuring a better contact with

the measurement probes, also serves as a self aligned mask for the removal of redundant PEDOT:PSS by reactive ion etching (O2 plasma). This step eliminates any parasitic currents

from top to bottom electrode. Current-voltage (I-V) measurements were performed in a home-built probe station using a

Keithley 4200 Semiconductor Analyzer Characterization System. The probe station was pressurized at 10-6-10-7 mbar for at least 6 hours before the measurements, to remove any water

absorbed in the PEDOT:PSS layer. Devices were swept in the voltage range of 0 V to 1 V to -1 V and back to 0 V and the recorded current densities were averaged for all devices with different

diameters. We measured in total 27-36 devices per SAM and found nearly identical current densities for junctions of 5-100 µm in diameter. We have plotted the median of the current

density as function of the voltage.

5.9.5 MCBJ Measurements Bern57

A notched gold wire (0.1 mm diameter) was glued on a polyimide-coated stainless steel sample with epoxy glue (stycast 2850ft with catalyst 9) and cleaned in an ozone cleaner. A liquid cell

was mounted on the sample and a mM solution of molecular wires in THF/decane (1:4) was placed in the liquid cell under argon atmosphere. The substrate was bend by a pushing rod,

controlled by a stepper motor and a piezo stack. After breaking of the junction, current-distance traces were recorded while repeatedly opening and closing.

159

Chapter 5

5.10 References and Notes1. N.F. Phelan, M. Orchin, J. Chem. Educ. 1968, 45, 633.

2. C.A. van Walree, V.E.M. Kaats-Richters, S.J. Veen, B. Wieczorek, J.H. van der Wiel, B.C. van der Wiel, Eur. J. Org. Chem. 2004, 3046-3056.


4. D.Q. Andrews, G.C. Solomon, R.H. Goldsmith, T. Hansen, M.R. Wasielewski, R.P. Van Duyne, M.A. Ratner, J. Phys. Chem. C 2008, 112, 16991-16998.


6. P. Rocheleau, M. Ernzerhof, J. Chem. Phys. 2009, 130, 184704.

7. M. Kiguchi, H. Nakamura, Y. Takahashi, T. Takahashi, T. Ohto, J. Phys. Chem. C 2010, 114, 22254-22261.

8. J.R. Quinn, F.W. Foss, L. Venkataraman, M.S. Hybertsen, R. Breslow, J. Am. Chem. Soc. 2007, 129, 6714-6715.

9. S.N. Yaliraki, M.A. Ratner, Ann. NY Acad. Sci. 2002, 960, 153-162.

10. G.C. Solomon, D.Q. Andrews, R.P. Van Duyne, M.A. Ratner, ChemPhysChem 2009, 10, 257-264.

11. J.M. Tour, M. Kozaki, J.M. Seminario, J. Am. Chem. Soc. 1998, 120, 8486-8493.

12. J.C. Ellenbogen, J.C. Love, Proc. IEEE 2000, 88, 386-426.

13. M.H. van der Veen, M.T. Rispens, H.T. Jonkman, J.C. Hummelen, Adv. Funct. Mater. 2004, 14, 215-223.

14. M.H. van der Veen, PhD Thesis "π-Logic" University of Groningen, 2006.

15. M. Irie, Chem. Rev. 2000, 100, 1685-1716.

16. D. Dulić, S.J. van der Molen, T. Kudernac, H.T. Jonkman, J.J.D. de Jong, T.N. Bowden, J. van Esch, B.L. Feringa, B.J. van Wees, Phys. Rev. Lett. 2003, 91, 207402; S.J. van der Molen, H. van der Vegte, T. Kudernac, I. Amin, B.L. Feringa, B.J. van Wees, Nanotechnology 2006, 17, 310-314; N. Katsonis, T. Kudernac, M. Walko, S.J. van der Molen, B.J. van Wees, B.L. Feringa, Adv. Mater. 2006, 18, 1397-1400; J. He, F. Chen, P.A. Liddell, J. Andréasson, S.D. Straight, D. Gust, T.A. Moore, A.L. Moore, J. Li, O.F. Sankey, S.M. Lindsay, Nanotechnology 2005, 16, 695-702.

17. A.J. Kronemeijer, H.B. Akkerman, T. Kudernac, B.J. Wees, B.L. Feringa, P.W.M. Blom, B. de Boer, Adv. Mater. 2008, 20, 1467-1473;


19. M. Zhuang, M. Ernzerhof, J. Chem. Phys. 2009, 130, 114704.

20. E.H. van Dijk, D.J.T. Myles, M.H. van der Veen, J.C. Hummelen, Org. Lett. 2006, 8, 2333-2336.

21. T. Markussen, J. Schiotz, K.S. Thygesen, J. Chem. Phys. 2010, 132, 224104.

22. G.C. Solomon, D.Q. Andrews, T. Hansen, R.H. Goldsmith, M.R. Wasielewski, R.P. Van Duyne, M.A. Ratner, J. Chem. Phys. 2008, 129, 054701.

160

23. T. Markussen, R. Stadler, K.S. Thygesen, Nano Lett. 2010, 10, 4260-4265.

24. G.C. Solomon, D.Q. Andrews, R.P. Van Duyne, M.A. Ratner, J. Am. Chem. Soc. 2008, 130, 7788-7789; G.C. Solomon, D.Q. Andrews, R.H. Goldsmith, T. Hansen, M.R. Wasielewski, R.P. Van Duyne, M.A. Ratner, J. Am. Chem. Soc. 2008, 130, 17301-17308.

25. R. Baer, D. Neuhauser, J. Am. Chem. Soc. 2002, 124, 4200-4201.

26. A.A. Kocherzhenko, F.C. Grozema, L.D.A. Siebbeles, J. Phys. Chem. C 2010, 114, 7973-7979.

27. R. Stadler, Phys. Rev. B 2009, 80, 125401.

28. N. Renaud, M. Ito, W. Shangguan, M. Saeys, M. Hliwa, C. Joachim, Chem. Phys. Lett. 2009, 472, 74-79.

29. D.M. Cardamone, C.A. Stafford, S. Mazumdar, Nano Lett. 2006, 6, 2422-2426; C.A. Stafford, D.M. Cardamone, S. Mazumdar, Nanotechnology 2007, 18, 424014.

30. S. Ke, W. Yang, H.U. Baranger, Nano Lett. 2008, 8, 3257-3261.

31. D.Q. Andrews, G.C. Solomon, R.P. Van Duyne, M.A. Ratner, J. Am. Chem. Soc. 2008, 130, 17309-17319.

32. A.B. Ricks, G.C. Solomon, M.T. Colvin, A.M. Scott, K. Chen, M.A. Ratner, M.R. Wasielewski, J. Am. Chem. Soc. 2010, 132, 15427-15434.

33. J. Thome, M. Himmelhaus, M. Zharnikov, M. Grunze, Langmuir 1998, 14, 7435-7449.

34. C.D. Bain, G.M. Whitesides, J. Phys. Chem. 1989, 93, 1670-1673.35. The thicknesses as obtained by ellipsometry and XPS are averaged: The absolute values

obtained from XPS by method A are considered more thrust worthy than those obtained by method B and therefore weighed twice as strong. Identical weights were used for ellipsometry and XPS (methods A and B combined). The value for AC-DT determined by ellipsometry and the value for AQ-DT determined by XPS method A are not included in the average.

36. We have not investigated the quality of these SAMs by electrochemistry. We assume that these SAMs are densely packed and of high-quality, since we used the optimized procedure developed in Chapter 3.

37. CP-AFM measurements were performed by Constant Guédon and Sense Jan van der Molen at Leiden Univerity.


39. DFT transport calculations were performed by Troels Markussen and Kristian Thygesen at the Technical University of Denmark.

40. J.J. Mortensen, L.B. Hansen, K.W. Jacobsen, Phys. Rev. B 2005, 71, 035109.

41. A.H. Larsen, M. Vanin, J.J. Mortensen, K.S. Thygesen, K.W. Jacobsen, Phys. Rev. B 2009, 80, 195112.

42. J. Enkovaara, C. Rostgaard, J.J. Mortensen, J. Chen, M. Du ak, L. Ferrighi, J. Gavnholt, C.ł Glinsvad, V. Haikola, H.A. Hansen, H.H. Kristoffersen, M. Kuisma, A.H. Larsen, L. Lehtovaara, M. Ljungberg, O. Lopez-Acevedo, P.G. Moses, J. Ojanen, T. Olsen, V. Petzold, N.A. Romero, J. Stausholm-Møller, M. Strange, G.A. Tritsaris, M. Vanin, M. Walter, B. Hammer, H. Häkkinen, G.K.H. Madsen, R.M. Nieminen, J.K. Nørskov, M. Puska, T.T. Rantala, J. Schiøtz, K.S. Thygesen, K.W. Jacobsen, J. Phys.: Condens. Matter 2010, 22, 253202.

43. EGaIn measurements were performed in our group by Davide Fracasso and Ryan Chiechi, University of Groningen.

161



45. The histograms are automatically fit to a Gaussian distribution using the least-squares fitting routine from GnuPlot.

46. For a detailed discussion on the analysis of the data see: D. Fracasso, H. Valkenier, J.C. Hummelen, G.C. Solomon, R.C. Chiechi, submitted for publication

47. D. Porath, Y. Goldstein, A. Grayevsky, O. Millo, Surf. Sci. 1994, 321, 81-88.

48. C.A. Nijhuis, W.F. Reus, G.M. Whitesides, J. Am. Chem. Soc. 2009, 131, 17814-17827.

49. K.S. Wimbush, W.F. Reus, W.G. van der Wiel, D.N. Reinhoudt, G.M. Whitesides, C.A. Nijhuis, A.H. Velders, Angew. Chem. Int. Ed. 2010, 49, 10176-10180.

50. E.A. Weiss, G.K. Kaufman, J.K. Kriebel, Z. Li, R. Schalek, G.M. Whitesides, Langmuir 2007, 23, 9686-9694.


52. M.M. Thuo, W.F. Reus, C.A. Nijhuis, J.R. Barber, C. Kim, M.D. Schulz, G.M. Whitesides, J. Am. Chem. Soc. 2011, 133, 2962-2975.

53. F. Scharmann, G. Cherkashinin, V. Breternitz, C. Knedlik, G. Hartung, T. Weber, J.A. Schaefer, Surf. Interface Anal. 2004, 36, 981-985.

54. Large Area Molecular Junctions were made and analyzed by Ilias Katsouras in the group of Dago de Leeuw, Zernike Insitute for Advanced Materials, University of Groningen.

55. H.B. Akkerman, P.W.M. Blom, D.M.D. Leeuw, B.D. Boer, Nature 2006, 441, 69-72.

56. A.J. Kronemeijer, E.H. Huisman, I. Katsouras, P.A. van Hal, T.C.T. Geuns, P.W.M. Blom, S.J. van der Molen, D.M. de Leeuw, Phys. Rev. Lett. 2010, 105, 156604.

57. MCBJ measurements were performed by Wenjing Hong, in the group of Thomas Wandlowski at the Univerity of Bern.

58. UHV MCBJ studies are in progress by Diana Dulić and Mickael Perrin in the group of Herre van der Zant at Delft University of Technology.

59. We cannot exclude the possibility that some of the relatively unstable H2AC molecules have been converted in situ into 26AC and cause the small peak at 10-4.7 G0 in the histogram of H2AC.

60. C.A. Martin, D. Ding, H.S.J. van der Zant, J.M. van Ruitenbeek, New J. Phys. 2008, 10, 065008.

61. WinSpec 2.09, developed at Laboratoire Interdépartemental de Spectroscopie Electronique, Namur, Belgium

162

Chapter 5

Chapter 6Methano[10]annulene in Molecular Wires and Polymers

We have synthesized 2,7-dibromo-9,10-methano[10]annulene and incorporated this building block in a molecular wire to study the influence of this ten π-electron aromatic building block on the conductance of the wire. We found that the HOMO-LUMO gap of this wire is smaller than that of its naphthalene analogue.

We have incorporated methano[10]annulene in a copolymer with didecylbithiophene and compared this to similar copolymers with either naphthalene or benzothiadiazole incorporated. The optical band gap of the methano[10]annulene-based copolymer was found in between those of the other two polymers, though all band gaps were larger than expected, which we attribute to a torsion angle in the backbone of the polymers.

163

Chapter 6

6.1 IntroductionIn Chapters 4 and 5 we have investigated the influence of the incorporation of

various building blocks in molecular wires: acenes of increasing size (i.e., benzene,

naphthalene, and anthracene) and different conjugation patterns. The ultimate aim

of this Chapter was to investigate the influence of aromaticity on the conductance

of π-conjugated molecular wires. We compare two linear conjugated building

blocks: 2,7-disubstituted 1,6-methano[10]annulene and 1,5-disubstituted

naphthalene (Figure 6.1). Both have 10 π-electrons, either in one or two rings of sp2

hybridized carbon atoms, which gives rise to a difference in aromaticity.

Furthermore, having synthesized the methano[10]annulene building block, we

expand the scope of this thesis on molecular wires and their conductance, by

incorporating this building block in π-conjugated polymers to study their

conductivity in films, in line with other ongoing research in our group.

6.1.1 Aromaticity

In Chapter 1.2 we have explained the concept of π-conjugation, in which the pz-

orbitals of sp2 hybridized carbon atoms combine into molecular orbitals. This was

illustrated with 1,3,5-hexatriene in Figure 1.2, for which six molecular orbitals

were obtained with an increasing number of nodal planes (from zero to five) and a

corresponding increase in energy (Figure 6.2). However, for an annulene molecule,

of which the sp2 hybridized carbon atoms form a cycle, nodal planes can be drawn

in different ways, resulting in degenerate molecular orbitals. The most famous

example is benzene, which has two degenerate HOMOs (with one nodal plane

each) and two degenerate LUMOs (with two nodal planes each), besides a bonding

orbital in which all pz orbitals have an identical symmetry (this orbital is the lowest

in energy) and an anti-bonding orbital which has three nodal planes that cross each

164

Figure 6.1 a. 2,7-disubstituted 1,6-methano[10]annulene, b. 1,5-disubstituted naphthalene.

Methano[10]annulene in Molecular Wires and Polymers

other in the center of the molecule (this orbital is the highest in energy). Thus, as

shown in Figure 6.2, the six molecular π-orbitals of benzene correspond to only

four different energy levels, where the six orbitals of hexatriene correspond to six

energy levels. This results in a larger energy difference between the HOMO and the

LUMO of benzene compared to hexatriene. Furthermore, the overall energy of

benzene is lower than of hexatriene, which is called "aromatic stabilization". From

a valence-bond theory perspective, this can be understood by the presence of the

resonance structures that are equal in energy (see Figure 6.2).

A molecule is considered to be aromatic when it has 4n+2 π-electrons in one

(nearly) planar ring of all sp2 hybridized atoms, according to Hückel's rule.1 The

origin of this 4n+2 rule can be found in the energy diagram of benzene in Figure

6.2: if we would add two more electrons (4n), these have to be placed in each of

the two empty degenerate orbitals according to Hund's rule, resulting in an open

shell compound with two unpaired electrons. Addition of another two electrons

results in a closed- shell compound with 10 π-electrons.

6.1.2 Methano[10]annulene

After benzene with 6 π-electrons (C6H6), the first neutral aromatic compound

would be [10]annulene, a ring structure with the molecular formula C10H10.

However, this structure is not planar and has not sufficient overlap between the p z-

orbitals to satisfy Hückel's rule; [10]annulene is therefore not aromatic.2 In 1964

Vogel and Roth reported the synthesis of 1,6-methano[10]annulene, in which a

CH2-bridge was used to force the [10]annulene structure into a nearly planer

geometry (Figure 6.1).3 Vogel and Roth reported a 1H NMR spectrum with

resonances from eight protons between 7.5-6.8 ppm and two at -0.5 ppm. This

165

Figure 6.2 Energy levels of the π-orbitals of 1,3,5-hexatriene (left) and benzene (right).

Chapter 6

indicates the presence of a ring current, resulting in shielding of the protons at the

methano group and deshielding of the protons outside the ring. The presence of

such a ring current in a magnetic field is a strong indication for aromaticity.

Another indication for the aromaticity of methano[10]annulene is obtained from

crystallographic data, which show a symmetric structure in which the lengths of

opposite carbon-carbon bonds in the ten-membered ring differ less that 1%. 4

Besides classical aromaticity, also homoaromaticity5 has been found for

methano[10]annulene: through space interactions between orbitals on both sides of

the methano bridge give rise to a small additional stabilization.6,7

Recently, methano[10]annulene has been incorporated in conjugated structures for

OLED applications,8 in molecular wires with and without donor-acceptor groups,9

in quinoidal structures,10 and in electrochemically synthesized copolymers with

thiophene11,12 or furan.13 Peart and Tovar performed spectroelectrochemical

experiments on these polymer films and concluded that the effective conjugation is

significantly larger in the polymers with 2,7-disubstituted methano[10]annulene

incorporated than in those with 1,5-disubstituted naphthalene. They attribute this

to the olefinic character of methano[10]annulene that is present in addition to its

aromatic character12 (which is less pronounced compared to naphthalene7). The

smaller HOMO-LUMO gap found for methano[10]annulene compared to

naphthalene is also attributed to its partial olefinic character. Thus,

methano[10]annulene is found to have some degree of aromatic stabilization and

other aromatic properties (compare to right part of Figure 6.2), combined with

olefinic properties, as found in hexatriene (Figure 6.2 left) and in polyacetylene.

The conductivity of polyacetylene can be tuned over a very wide range by doping,14

however, the problematic stability of the polymer limits its applications. Its olefinic

nature, combined with aromatic stabilization, makes methano[10]annulene an

interesting building block to study in our dithiolated molecular wires for

conductance measurements (Section 6.3) and in soluble thiophene-based

copolymers (Section 6.4).

6.2 Synthesis of 2,7-Dibromo-1,6-methano[10]annuleneAs mentioned above, the synthesis of 1,6-methano[10]annulene 6.3 was first

166


reported by Vogel and Roth in 1964.3 The strategy for the synthesis of 6.3, which

has been reported in detail in Organic Synthesis,15 is outlined in Scheme 6.1.

Naphthalene was reduced to isotetralin 6.1 in a Birch reduction in 75-80% yield.

Dichlorocarbene was generated from chloroform and potassium tert-butoxide and

added to the central double bond of 6.1 in 40-45%. Subsequently, the chlorine-

atoms were removed in another Birch reduction, resulting in compound 6.2 in 85-

90%. Compound 6.2 was in the original report from Vogel and Roth3 converted

into the aromatic target compound 6.3 by a bromination, followed by a

dehydrobromination. Instead, 2,3-dichloro-5,6-dicyano-1,6-benzoquinone (DDQ)

can be used to convert 6.2 into 6.3 in 85-90%, as reported by Nelson and Untch in

196916 and included in the Organic Synthesis procedure.15

Although this Organic Synthesis procedure is widely used for the synthesis of 1,6-

methano[10]annulene,11,12 the handling of large volumes of liquid ammonia for the

Birch reductions and the purification of the dichlorocarbene adduct were highly

time consuming.17 For that reason, we used an alternative method. We reduced

naphthalene into isotetralin 6.1 using lithium in ethylenediamine and n-propyl

amine cooled with an ice-salt bath according to the recently reported procedure of

Garst et al.18 and obtained 6.1 in 56% (Garst et al. reported 74% yield). Then we did

an addition of methylene (:CH2) onto 6.1 in a modified Simmons-Smith

reaction,16,19 which yielded a mixture of products, consisting of 6.2 (30-50%), its

isomer with the carbene added on one of the other double bonds (1-30%), the bis-

adduct (10-50%), and traces of tetralin and Δ2-decalin. Instead of isolating 6.2

from this mixture (which is very difficult), we treated the mixture of compounds

with DDQ in the next step, which yielded, after purification by column

chromatography, a mixture of methano[10]annulene 6.3 and naphthalene.20 This

mixture is not easily separated, due to similar boiling points and co-crystallization

167

Scheme 6.1 Synthesis of methano[10]annulene: (i) Na, NH3, EtOH, Et2O, -78°C; (ii) CHCl3, KOtBu, -30-0°C; (iii) Na, NH3, MeOH, Et2O, -78°C; (iv) DDQ, AcOH, dioxane, reflux; (v) Li, (CH2NH2)2, n-PrNH2, tBuOH, 0°C; (vi) Zn, CuCl, MeI2, Et2O, reflux.

Chapter 6

of the two compounds. We should note that solutions containing 6.3 and its

precursors are better not concentrated by rotary evaporation, since their high vapor

pressures cause the compounds to evaporate together with the solvent to be

removed.

Treatment of the mixture of methano[10]annulene 6.3 and naphthalene with N-

bromosuccinimide (NBS) resulted in selective bromination of 6.3 into 2-bromo-

1,6-methano[10]annulene 6.4, which was in a second treatment with NBS

converted into 2,7-dibromo-1,6-methano[10]annulene 6.5.21,22 Apart from the

desired 2,7-dibromo compound 6.5, its isomer 2,5-dibromo-1,6-

methano[10]annulene can be formed, especially when 6.3 is directly treated with

two equivalents of NBS. The boiling point of 6.4 and 6.5 is significantly increased

compared to that of naphthalene and 6.3, thus naphthalene can be easily removed

by distillation. After recrystallization, we obtained pure 6.5 (in 3.5% overall yield

from isotetralin), which was incorporated into molecular wires and conjugated

polymers.

6.3 Methano[10]annulene-Based Molecular Wire

6.3.1 Synthesis of the Molecular Wires

We have synthesized methano[10]annulene-based molecular wire 6.6A (Scheme

6.3), which consists of a 2,7-disubstituted-1,6-methano[10]annulene core unit,

phenylene ethynylene spacers and thioacetate end groups, to anchor the molecule

to gold electrodes (see Chapter 1.5). To compare the special aromatic

methano[10]annulene unit with the more common naphthalene unit, we

synthesized molecular wire 6.7A as a reference compound. Wires 6.6A and 6.7A

are similar to reported wires, apart from the acetyl-protected thiol anchoring

168

Scheme 6.2 Bromination of methano[10]annulene: (i) NBS, CH2Cl2, 0°C-reflux.


groups.23,9,11 Wire 6.7B was synthesized in two steps by a Sonogashira cross-

coupling of 1,5-diiodonaphthalene24 and 1-tert-butylthio-4-ethynylbenzene 2.13

(see Chapter 2.2) in 77% and subsequently converted with into 6.7A in 85%, using

boron tribromide and acetyl chloride.25

Methano[10]annulene wire 6.6A was synthesized according to the same strategy.

The synthesized 2,7-dibromo-1,6-methano[10]annulene 6.5 was cross-coupled with

acetylene 2.13 to give 6.6B in 47% yield. The reaction of 6.6B with boron

tribromide (20 equivalents) and acetyl chloride according to the standard

procedure25 gave a mixture of products, similar to our results for the conversion of

anthracene wire 4.5B into 4.5A (see Chapter 4.2). We therefore adopted the

procedure that was used to convert 4.5B into 4.5A, by adding only two equivalents

of boron tribromide to a solution of 6.6B at 0°C.26 However, besides the desired

6.6A, a side product was formed, which showed an additional signal at 2.32 ppm

in the 1H NMR spectrum and the signal from the methylene group was split into a

doublet, indicating that an asymmetric compound was formed. Furthermore,

many small signals in the aromatic region were found. We attribute these

additional signals in the 1H NMR spectrum to a molecule similar to 6.6A, with an

additional acetyl group at the methano[10]annulene core, which can be formed by

a Friedel-Crafts acylation.27 We have not succeeded in the separation of this

compound (35-38%) from target wire 6.6A.

As for wire 4.5A, the synthetic difficulties in obtaining 6.6A pure are attributed to

the relatively low HOMO-LUMO gap of the compound (see Section 6.3.2), which

increases its reactivity. An alternative approach to the synthesis of 6.6A could be

by a Sonogashira cross-coupling of 6.5 and 4-ethynyl-1-thioacetylbenzene 2.10,

although coupling of this acetylene with 9,10-dibromoanthracene in an attempt to

169

Scheme 6.3 Syntheses of molecular wires 6.5 and 6.6: (i) Pd(PPh3)2Cl2, CuI, iPr2NH, THF, reflux; (ii) BBr3, AcCl, CHCl3, toluene.

Chapter 6

synthesize 4.5A gave only 5% yield.26 The yield of this coupling might be increased

by the use of a more active diiodo-compound instead of a dibromo-compound.

2,7-Diiodo-9,10-methano[10]annulene has not been reported yet. Alternatively, the

use of other thiol protecting groups or alternative anchoring groups can be

explored.

6.3.2 UV-Vis Absorption Spectra

We have measured the UV-Vis absorption spectra of compounds 6.6B and 6.7B

(Figure 6.3). In good agreement with the absorptions that were measured for the

compounds without the tert-butyl thioethers,11 the absorption of the

methano[10]annulene-containing wire 6.6B is redshifted by 33 nm compared to

the absorption of naphthalene wire 6.7B. The optical HOMO-LUMO gaps as

determined from the onset of the absorptions are 2.81 eV for 6.6B and 3.23 eV for

6.7B. This is in good agreement with the relatively low aromatic stabilization of

methano[10]annulene, when compared to naphthalene (as described in Section

6.1.2). Based on the trends that we observed in Chapter 4, we expect a higher

conductance for methano[10]annulene wire 6.6 than for naphthalene-wire 6.7.28

170

Figure 6.3 Normalized UV-Vis absorption spectra of molecular wires 6.6B (black) and 6.7B (gray) as 10-5M solutions in CH2Cl2.


6.4 Copolymer of Methano[10]annulene and BithiopheneIn the aforementioned work of Peart and Tovar, 2,7-dibromo-1,6-

methano[10]annulene 6.5 was cross-coupled with bithiophene units and the

resulting monomer was polymerized electrochemically.11 Electrochemical doping

(oxidation) of this polymer resulted in a decrease of its optical absorption at 480

nm and the appearance of an absorption around 875 nm, whereas the

naphthalene-analogue of this polymer showed a decreasing absorption at 430 nm

and an increasing absorption at 650 nm upon oxidation. The 200 nm difference

between the new absorptions was attributed to the improved delocalization of the

generated carbocation in the methano[10]annulene-quarterthiopene copolymer.

These experiments showed the potential for copolymers of thiophene and

methano[10]annulene as conductive polymers for organic electronics. However, for

organic electronic purposes soluble polymers are preferred.

In our group, Frank Brouwer has established a method to improve the quality of

soluble conjugated copolymers which consist of a bithiophene and another

conjugated unit by the use of bis(pinacolato)diboron (BiPi) in a Suzuki-type

polymerization.29,30,31 For that reason, we have incorporated methano[10]annulene

in this conjugated copolymers as shown in Figure 6.4. The quality of the

copolymers synthesized by this "BiPi-method" is higher compared to other

polymerization methods, because the polymerization itself is a

homopolymerization. The conjugated building blocks are functionalized with two

decylthiophene units, subsequently brominated, and polymerized upon in situ

formation of the boronic esters (Scheme 6.4).29 A more common approach is to

copolymerize a dibromo-functionalized monomer with a bis(trimethylstannyl)- or

bis(boronic ester)-functionalized monomer.32 However, this leads to a great

diversity in end-groups of the polymers33 and non-balanced amounts of both

171

Figure 6.4 The copolymers of methano[10]annulene (PTM), naphthalene (PTN), and benzothiadiazole (PTB) with didecyl-bithiophene, which are described in this Chapter.

Chapter 6

monomers can result in lower molecular weights.

We have synthesized poly(2,7-bis(3-decylthiophen-2-yl)-1,6-methano[10]annulene)

(PTM) and its naphthalene-analogue poly(1,5-bis(3-decylthiophen-2-

yl)naphthalene) (PTN). Furthermore, we have synthesized poly(4,7-bis(3-

decylthiophen-2-yl)-2,1,3-benzothiadiazole) (PTB), since benzothiadiazole is a well

known building block for small band gap polymers.34,35

6.4.1 Synthesis of the Monomers

Monomers 6.8, 610, and 6.12 were synthesized by a Kumada coupling: the

Grignard reagent of 2-bromo-3-decylthiophene was formed in a separate flask and

transferred into a solution of nickel catalyst and 2,7-dibromo-9,10-

methano[10]annulene, 1,5-diiodonaphthalene,24 or 4,7-dibromo-2,1,3-

benzothiadiazole.36 These Kumada couplings afforded methano[10]annulene

monomer 6.8 in 62% yield and naphthalene monomer 6.10 in 47% yield. The

Kumada coupling with 4,7-dibromo-2,1,3-benzothiadiazole to form monomer 6.12

was less successful and gave only 9% yield after two subsequent coupling steps (see

Experimental Section 6.6.3). Though a yield of 55% has been reported for the

Kumada coupling of 2-bromo-3-decyloxythiophene and 4,7-dibromo-2,1,3-

172

Scheme 6.4 Syntheses of polymers PTM, PTN, and PTB via the BiPi-method: (i) 3-decyl-2-thienylmagnesium bromide, Ni(dppp)Cl2, THF, toluene, reflux; (ii) NBS, THF, 0-20°C; (iii) bis(pinacolato)diboron, Pd(dppf)Cl2, K3PO4, DMF, toluene, 110-120°C.


benzothiadiazole,37 the Suzuki coupling is more widely applied in the synthesis of

hexyl-analogues of 6.12.36,38 The brominations of monomers 6.8, 6.10, and 6.12

with NBS to obtain 6.9, 6.11, and 6.13 respectively were performed successfully.

6.4.2 BiPi-Polymerizations

The three brominated monomers 6.9, 6.11, and 6.13 were polymerized according

to the BiPi-method, using bis(pinacolato)diboron, palladium-catalyst and the base

173

Figure 6.5 MALDI-TOF mass spectra of polymers PMT (a, b), PNT (c, d), and PBT (e, f).

Chapter 6

K3PO4.29 We determined the molecular weights by gel permeation chromatography

(GPC) -though this is known to overestimate the weights of conjugated polymers-

and found similar values for PTM (Mn = 6.2 ۟ kg/mol, Mw = 23 kg/mol) and PTN

(Mn = 11 kg/mol, Mw = 33 kg/mol), though significantly lower values for PTB (Mn

= 2.9 kg/mol, Mw = 4.7 kg/mol), which was furthermore obtained in low yield

(44% versus ~90% for PTM and PTN). Additional information was obtained from

the MALDI-TOF mass spectra of these polymers, which show the end-group

distributions of the polymers (Figure 6.5). For polymer PTM we did not observe

any brominated chains, whereas polymer PTN consisted of proton-terminated

chains (H-Xn-H) and a significant amount of bromine-terminated (Br-Xn-H) chains.

Assuming that direct debromination does not take place, bromine atoms are first

replaced by boronic esters and proton-terminated chains are formed upon

deboronation. In the DMF/toluene solvent mixture that we used, deboronation

was also found for poly(3,3'-didecyl-quarterthiophene).29 We attribute the small

signal with an additional mass of 127 (in the spectrum of PTM in Figure 6.5b) to

one boronic ester group (indicating incomplete deboronation) and the additional

mass of 90 could originate from the addition of a toluene radical to the polymer.

Significant amounts of Br-Xn-H being found for PTN could be due to the fast

reaction of the monoboronated monomer in the Suzuki coupling (see ref. 29 for

details).

In the MALDI-TOF mass spectrum of PTB we found mainly polymer chains with

two bromine end groups (Br-Xn-Br), besides Br-Xn-H, chains that had reacted with

the terthiophene matrix (+167), and oxidized chains (+32). The combination of

the low yield, low molecular weight and high percentage of Br-Xn-Br indicates that

the replacement of bromine groups by boronic esters is seriously suppressed, due

to the electron-poor nature of the benzothiadiazole unit.

6.4.3 UV-Vis Absorption and Fluorescence Spectra

We have measured the UV-Vis absorption and the fluorescence spectra of the

polymers PTM, PTN, and PTB. The naphthalene-based copolymer PTN was

isolated as a light gray powder, in agreement with an absorption maximum at only

358 nm and optical band gap of 3.10 eV. The methano[10]annulene-based

copolymer PTB shows an absorption maximum at 423 nm and an optical band gap

of 2.47 eV. This band gap is lower than that of PTN, as predicted, but not as low as

that of the benzothiadiazole-based copolymer PTB, which has a maximum at 474

174


nm and an optical band gap of only 2.20 eV. The fluorescence spectra show the

same trend, with emission maxima at 446 nm, 563 nm, and 656 nm for PTN,

PTM, and PTB respectively.

The optical band gaps of the soluble polymers PTM and PTN are significantly

larger than those of the methano[10]annulene- and naphthalene-containing

electrochemically polymerized films of Peart and Tovar (~2.0 and 2.4 eV

respectively).11 This difference is not caused by the difference in the number of

thiophene units between the methano[10]annulene or naphthalene units, as can be

concluded from a comparison of the electrochemically formed polymers with

either two or four repeating thiophene units, for which the band gaps differ only

marginally.12 Most likely, the difference between our polymers and the

electrochemically polymerized films is caused by the solubilizing decyl chains,

which cause the thiophene units to bend out of the plane of the naphthalene or

methano[10]annulene π-system, introducing a torsion angle ( ) in the polymerθ

backbone (Figure 6.7a). This torsion angle decreases the π-overlap and results in

larger band gaps. The polymer backbone is expected to be less twisted when

175

Figure 6.7 a. The solubilizing decyl chains on the thiophenes introduce a torsion angle ( ) in theθ backbone of the polymer, increasing its band gap. b. In this second generation methano[10]annulene polymer, which contains additional thiophene units, this torsion angle is expected to be smaller.

Figure 6.6 Normalized UV-Vis absorption spectra of polymers PMT, PNT, and PBT (solid lines) and normalized fluorescence spectra of these polymers (dashed lines) as solutions in CHCl3.

Chapter 6

additional thiophene rings are introduced between the decyl-functionalized

thiophene units and the naphthalene or methano[10]annulene units (Figure 6.7b).39

6.5 ConclusionsWe have developed a convenient, though not high yielding, synthetic protocol for

2,7-dibromo-9,10-methano[10]annulene and incorporated this building block in a

molecular wire, which we compared with an analogous naphthalene-based wire. In

the UV-Vis absorption spectra, we found a redshift of the methano[10]annulene-

based wire compared to the naphthalene-based wire, which is a clear indication

that methano[10]annulene, though being a ten π-electron aromatic system, has less

aromatic stabilization compared to naphthalene. We expect therefore a higher

conductance for the methano[10]annulene-wire than for the naphthalene-wire.

However, its relatively small HOMO-LUMO gap increased the reactivity of the

methano[10]annulene-wire, which resulted in the formation of a side-product in

the final step of the synthesis. We have not been able to isolate the pure

methano[10]annulene-wire with thioacetate end groups and suggest to follow an

alternative synthetic approach towards methano[10]annulene-based wires.

We have incorporated the methano[10]annulene moiety successfully into soluble

conjugated copolymers with didecyl-bithiophene, according to the strategy that

was recently developed in our group. We compared the methano[10]annulene-

based copolymer with naphthalene- and benzothiazole-based copolymers and

found its band gap to be in between. We attribute the larger than expected band

gap to a torsion angle in the backbone, caused by the solubilizing decyl chains. We

suggest to incorporate additional non-substituted thiophene units to prevent the

backbone of the polymer from twisting. Preliminary mobility measurements that

compared methano[10]annulene-based copolymer PTM with naphthalene-based

copolymer PTN in Field Effect Transistors gave a mobility of 8۟10· -6 cm2V-1s-1

(saturated regime), with a threshold voltage of -27 V and an on/off ratio of 10 3 for

PTM, whereas no transistor behavior was found for PTN.40 Better mobilities are

expected for the next generation methano[10]annulene-based copolymers. We

should note that the methano group of methano[10]annulene hinders the

crystallization of the monomers and polymers. A methano[10]annulene-based

polymer will therefore not adopt a crystalline structure in the film, which probably

limits the mobility of charge carriers in the polymer.

176



General

All reactions were performed under a nitrogen atmosphere, using oven-dried glassware (150°C) and dry solvents. NBS was recrystallized from water and all brominations were performed in the

dark. Diisopropylamine was distilled over NaOH. Copper iodide was heated and dried under vacuum. The catalysts used are: bis(triphenylphosphine)palladium(II) chloride (Pd(PPh3)2Cl2,

CAS: 13965-03-2), 1,1'-bis(diphenylphosphino)ferrocene-palladium(II)dichloride dichloro-methane complex (Pd(dppf)Cl2.CH2Cl2, CAS: 72287-26-4), [1,3-Bis(diphenylphosphino)propane]

nickel(II) chloride (Ni(dppp)Cl2, CAS: 15629-92-2).1,5-Diiodonaphthalene and 4,7-dibromo-2,1,3-benzothiadiazole were synthesized according to

the literature procedures.24,36 See Chapter 2 for the synthesis of 1-tert-butylthio-4-ethynylbenzene (2.13) and details on the analyses of organic compounds.

GPC measurements were performed on a Spectra Physics AS 1000 series machine equipped with a Viskotek H-502 viscometer and a Shodex RI-71 refractive index detector. The columns (PLGel

5 mixed-C, Polymer Laboratories) were calibrated using narrow disperse polystyrene standardsμ (Polymer Laboratories). Samples were made in CHCl3 at a concentration of 1 mg/mL. MALDI-

TOF measurements were performed on a Biosystems Voyager apparatus. Samples were prepared by mixing the matrix (terthiophene, 20 mg/mL in CHCl3) and the sample (1 mg/5 mL in

CHCl3) in a 1:1 ratio. All the samples were measured in negative ion mode.

6.6.1 Synthesis of 2,7-dibromo-9,10-methano[10]annulene

Isotetralin (6.1)

This compound was made by a modification of the literature procedure.18 Naphthalene (75.2 g, 0.59 mol), ethylenediamine (270 g, 4.5 mol), and tert-butanol (272 g, 3.6 mol)

were placed in a 3 L three-necked flask under nitrogen. The setup was cooled to -3°C with an ice-salt bath and n-propylamine (600 mL) was added. Pieces of lithium wire (25.3 g, 3.65 gram-

atoms) were added to the solution over 3 hours, while the temperature was kept below 20°C. The reaction mixture was stirred overnight, after which 1 L ice water was added. The mixture was

filtered to remove the white precipitate, layers were separated, and the aqueous layer was extracted with ether (2 x 600 mL). The combined organic layers were washed with water (2 x 600

mL) and brine (600 mL), dried over Na2SO4, filtered, and the solvent was removed under reduced pressure. The crude product was recrystallized from methanol, yielding 42 grams (0.32

mol, 56%) of 6.1 as white crystals.1H-NMR (200 MHz, CDCl3): 5.73 (s, 4H), 2.54 (s, 8H). δ 13C-NMR (50 MHz, CDCl3): 124.4,δ

123.3, 30.8.

1,6-Methano[10]annulene (6.3)

This compound was made by a modification of the literature procedure.16 Zinc (93 g,

177

Chapter 6

1.41 mol) and copper chloride (44 g, 0.44 mol) were placed in an oven-dried 3 L three-necked

flask and dry ether was added (750 mL). The suspension was refluxed for 40 minutes and methylene iodide (329 g, 1.23 mol) was added dropwise in 2 hours, upon which the mixture

foamed heavily and turned dark red. Ether was added (500 mL) to compensate the volume that was lost and the mixture was refluxed for another 2 hours. Then a solution of 6.1 (30 g, 0.23

mol) in ether (250 mL) was added dropwise in 15 minutes and the reaction mixture was refluxed for 16 hours. An aqueous solution of NH4Cl (100 mL) was added, followed by 2 M HCl (100

mL). The reaction mixture was filtered through cotton wool and pentane (300 mL) was used to rinse the flask. The resulting organic layer was washed with water (2 x 500 mL) and brine (350

mL), dried over Na2SO4, filtered, and concentrated to a volume of 200 mL. This yellow solution was run through a plug of silica gel, eluted with pentane. Around 80% of the solvent was

removed by rotary evaporation and the remaining solvent was distilled through a vigreux column at ambient pressure, to leave 36.3 g of a colorless liquid, which contained ~50% 6.2, as

determined by 1H NMR (CDCl3, 400 MHz): 5.52 (s, 4H), 2.31 (d, δ J = 15, 4H), 2.15 (d, J = 15, 4H), 0.58 (s, 2H).

Dioxane (900 mL) was distilled from KOH (45 g) into a 1 L three-necked flask. DDQ (110 g, 0.485 mol) was dissolved in the dioxane upon heating, to give a dark red solution. Crude 6.2 (36.2 g) was added to this solution and the reaction mixture was refluxed for 63 hours, after which 600 mL of the dioxane was removed by distillation through a vigreux column. The

remaining slurry was filtered through a glass filter and washed with warm pentane (500 mL), which resulted in the formation of a black precipitate in the filtrate. The filtrate was filtered

through cotton wool and all solvents were removed by distillation over a vigreux column. The resulting black liquid was purified by column chromatography (silica gel, pentane), yielding 11.2

g of a yellow liquid, which contained 5 g (35 mmol, 15% yield) 6.3, besides naphthalene and solvent, as determined by 1H NMR (CDCl3, 400 MHz): 7.45 (dd, δ J = 6.3, 2.2, 4H), 7.10 (dd, J = 6.2, 2.2, 4H), -0.44 (s, 2H). 13C-NMR (CDCl3, 50 MHz): 129.1, 126.5, 115.3, 35.3.δ

2,7-Dibromo-1,6-methano[10]annulene (6.5)

This compound was made by a modification of the literature procedure.22 A 3:1

mixture of methano[10]annulene and naphthalene (6.12 g, 34.0 mmol 6.3) was placed in an oven-dried 500 mL three-necked flask. CH2Cl2 (200 mL) was added and the

solution was cooled in an ice-salt bath. NBS (6.67 g, 37.5 mmol) was added and the reaction was stirred overnight at room temperature and refluxed for 5 hours. After cooling, the

reaction mixture was filtered through a plug of silica gel, eluted with CH2Cl2 and the solvent was removed by distillation through a vigreux column. The crude product was further purified by

column chromatography (silica gel, pentane) and removal of the pentane by distillation through a vigreux column yielded 6.04 g of yellow liquid, which contained 3.9 g (17.7 mmol) 6.4.1H-NMR (CDCl3, 400MHz): 7.76-7.72 (m, 1H), 7.43 (d, δ J = 8.8, 2H), 7.29 (d, J = 10, 1H), 7.23 (dd, J = 2.9, 6.2, 2H), 7.01 (t, J = 9.5, 1H), -0.29 (d, J = 10, 1H), -0.43 (d, J = 10, 1H).

The yellow liquid (6.03 g, 17.7 mmol 6.4) was placed in a 100 mL two-necked flask and CH2Cl2

(70 mL) and NBS (3.18 g, 17.9 mmol) were added, in the dark. The reaction mixture was

refluxed for 4 hours and stirred overnight at room temperature, after which it was filtered through a plug of silica gel, eluted with CH2Cl2. The solvent was removed by distillation through

a vigreux column and the naphthalene was removed by distillation in microdistillation setup at

178


70 mTorr. The residual dark brown oil was a mixture of 6.4 and 6.5, which was run over a

column of silica gel, eluted with pentane, after which the solvent was removed by distillation through a vigreux column. To the resulting 4.61 g yellow oil were added CH2Cl2 (50 mL) and

NBS (1.80 g, 10.1 mmol) and the mixture was refluxed for 15 hours in the dark. After cooling, the reaction mixture was filtered through a plug of silica gel, eluted with CH2Cl2 and the solvent

was removed by distillation through a vigreux column. The crude product was further purified by column chromatography (silica gel, pentane) and removal of the pentane by distillation

through a vigreux column yielded a yellow oil. This was recrystallized from ethanol (25 mL), yielding 2.31 g (7.70 mmol, 23% over two steps) of the title compound as yellow crystals.1H NMR (400 MHz, CDCl3): 7.71 (d, δ J = 9.0, 2H), 7.41 (d, J = 9.8, 2H), 7.13 (t, J = 9.4, 2H), -0.26 (s, 2H). 13C NMR (125 MHz, CDCl3): 130.77, 130.49, 129.28, 117.87, 114.45, 33.88. IRδ

(cm-1): 3039, 1900, 1715, 1519, 1446, 1383, 1219, 1153, 1010, 964, 951, 741, 917, 749, 702, 649.

6.6.2 Synthesis of Molecular Wires 6.6 and 6.7

2,7-Bis[(4-tert-butylthiophenyl)ethynyl]-1,6-methano[10]annulene (6.6B)

To a suspension of 6.5 (480 mg, 1.60 mmol), Pd(PPh3)2Cl2 (125 mg , 0.178 mmol), and copper iodide

(41.1 mg, 0.216 mmol) in THF (80 mL) were added diisopropylamine (16 mL) and 2.13 (764 mg, 4.01

mmol). The reaction mixture was refluxed for 15 hours, concentrated, and run over a plug of silica gel, eluted with CH2Cl2. The crude material was

preadsorbed onto silica gel and purified by column chromatography (silica gel, CH2Cl2/heptane 1:3), yielding 389 mg (0.750 mmol, 47%) of the title compound as a yellow oil.1H NMR (400 MHz, CDCl3): 7.83 (d, δ J = 8.6, 2H), 7.55 – 7.48 (m, 8H), 7.48 (d, J = 9.7, 2H), 7.21 (t, J = 9.1, 2H), 1.31 (s, 18H), -0.13 (s, 2H). 13C NMR (125 MHz, CDCl3): 137.27, 133.28,δ

132.09, 131.40, 130.04, 127.52, 123.67, 121.93, 118.00, 92.59, 88.70, 46.54, 35.00, 30.99. IR (cm-1): 2972, 2956, 2935, 2915, 2890, 2856, 2201, 1919, 1588, 1526, 1481, 1468, 1453, 1393,

1363, 1164, 1147, 1015, 830, 762. HRMS (APCI) calculated for [M+H]+ 519.2175, found 519.2161.

2.7-Bis[(4-acetylthiophenyl)ethynyl]-1,6-methano[10]annulene (6.6A)

6.6B (100 mg, 0.19 mmol) was dissolved in chloroform/toluene (1:1, 15 mL) and acetyl chloride

(0.55 mL) was added. The solution was cooled with an ice-salt bath and BBr3 (1 M in CH2Cl2, 0.50 mL, 0.50

mmol) was added slowly. The reaction mixture was stirred for 1 hour while cooled and for another 18 hours at room temperature, after which it was poured into ice water (200 mL). This

mixture was extracted with CH2Cl2 (4 x 50 mL), dried over Na2SO4, filtered, and all volatiles were removed by rotary evaporation. The crude material was preadsorbed onto silica gel and

purified by column chromatography (silica gel, CH2Cl2/heptane 2:1) yielding 56 mg (0.114 mmol, 60%) of the impure title compound as a red oil.

1H NMR (400 MHz, CDCl3): 7.83 (d, δ J = 8.7, 2H), 7.58 (d, J = 8.0, 4H), 7.49 (d, J = 9.6, 2H),

179

Chapter 6

7.41 (d, J = 8.0, 4H), 7.22 (t, J = 9.2, 2H), 2.44 (s, 6H), -0.13 (s, 2H); 2.32 (d, J = 2.6), - 0.25 (d, J = 8.7). 13C NMR (125 MHz, CDCl3): 193.47, 134.25, 132.17, 132.07, 130.13, 128.03, 127.56,δ 124.55, 121.76, 117.98, 92.35, 88.88, 34.98, 30.29, 29.69. IR (cm-1): 3032, 2920, 2851, 2200,

1907, 1702, 1590, 1484, 1396, 1350, 1113, 1087, 1014, 946, 824, 763, 606. HRMS (APCI) calculated for [M+H]+ 491.1134, found 491.1123.


To a suspension of 1,5-diiodonaphthalene (339 mg, 0.891 mmol), Pd(PPh3)2Cl2 (62.5 mg , 0.089 mmol), and copper

iodide (34.8 mg, 0.18 mmol) in THF (50 mL) were added diisopropylamine (10 mL) and 2.13 (567 mg, 2.28

mmol). The reaction mixture was refluxed for 20 hours, concentrated, and run over a plug of silica gel, which was eluted with CH2Cl2. The crude material was preadsorbed onto silica gel,

purified by column chromatography (silica gel, CH2Cl2/heptane 1:3), and recrystallized from heptane, yielding 342 mg (0.685 mmol, 77%) of the title compound as light yellow crystals.1H NMR (500 MHz, CDCl3): 8.45 (d, δ J = 8.5, 2H), 7.82 (d, J = 7.0, 2H), 7.64 – 7.54 (m, 10H), 1.33 (s, 18H). 13C NMR (125 MHz, CDCl3): 137.32, 133.55, 133.07, 131.53, 131.06, 127.14,δ

126.21, 123.55, 121.20, 94.18, 88.76, 46.57, 31.00. IR (cm -1): 2973, 2953, 2935, 2917, 2892, 2857, 2163, 1943, 1588, 1481, 1364, 1165, 1147, 1097, 1016, 833, 788, 609. HRMS (APCI)

calculated for [M+H]+ 505.2018, found 505.2005.



chloroform/toluene (1:1, 40 mL) and acetyl chloride (4 mL) was added. While stirring, BBr3 (1 M in CH2Cl2, 8

mL, 8 mmol) was added slowly. The reaction mixture was stirred for 4 hours and poured into ice water (400 mL). This was extracted with CH2Cl2 (4 x

200 mL), dried over Na2SO4, filtered, and all volatiles were removed by rotary evaporation. The crude material was preadsorbed onto silica gel and purified by column chromatography (silica

gel, CH2Cl2/heptane 2:1), yielding 164 mg (0.343 mmol, 85%) of the title compound as a light yellow solid.1H NMR (400 MHz, CDCl3): 8.44 (d, δ J = 8.6, 2H), 7.82 (d, J = 7.1, 2H), 7.71 – 7.65 (m, 4H), 7.59 (t, J = 7.7, 2H), 7.48 – 7.43 (m, 4H), 2.46 (s, 6H). 13C NMR (125 MHz, CDCl3): 193.42,δ

134.33, 133.07, 132.22, 131.19, 128.33, 127.23, 126.26, 124.45, 121.07, 93.94, 88.94, 30.32. IR (cm-1): 3044, 2923, 2192, 1924, 1683, 1590, 1483, 1396, 1360, 1135, 1113, 1091, 1014, 958, 822,

782, 627, 606. HRMS (APCI) calculated for [M+H]+ 477.0978, found 477.0963.

6.6.3 Synthesis of Monomers and Polymers PTM, PTN and PTB

3-Decylthiophene

This compound was synthesized according to a literature procedure.41 Magnesium (4.79 g, 197 mmol) was activated by stirring with glass shatters. 1-Bromodecane (43.17

mL, 195 mmol) in dry ether (125 mL) was added dropwise to the magnesium in dry

180


ether (60 mL) and the mixture was refluxed for 1 hour. Ni(dppp)Cl2 (125 mg, 0.24 mmol) and 3-

bromothiophene (21.3 g, 131 mmol) were suspended in dry ether (200 mL) and cooled with an ice-salt bath. The Grignard reagent was added via a cannula and the mixture was stirred for 3

days at room temperature. The reaction was quenched with water (125 mL), which caused the formation of solids and severe effervescence to occur. The mixture was extracted with pentane (3

x 150 mL) and the combined organic layers were washed with water (300 mL), dried over Na2SO4, filtered, and concentrated. Distillation under reduced pressure (3.60 mTorr; 125°C)

yielded 26.14 g of pure 3-decylthiophene (89% yield) as a colorless liquid. 1H-NMR (CDCl3, 400 MHz): 7.24 (dd, δ J = 2.4, J = 3.0, 1H); 6.93 (t, J=4.3 2H); 2.63 (t, J = 7.2

Hz, 2H); 1.66-1.57 (m, 2 H); 1.36-1.24 (m, 14H); 0.89 (t, J = 6.7 Hz, 3H). 13C-NMR (50 MHz, CDCl3): 143.50, 128.52, 125.24, 119.96, 32.14, 30.80, 30.52, 29.86, 29.85, 29.71, 29.58, 29.57,δ

22.53, 14.36.

2-Bromo-3-decylthiophene

This compound was synthesized according to a literature procedure.42 NBS (9.20 g,

51.3 mmol) was dissolved in DMF (40 mL) added dropwise to a solution of 3-decylthiophene (11.78 g, 52.5 mmol) in DMF (60 mL), cooled with an ice-salt bath.

The mixture was stirred overnight at room temperature, quenched with 2M HCl solution (200 mL) and extracted with CH2Cl2 (3 x 150 mL). The organic layers were washed with brine, dried

over Na2SO4, filtered, and the solvent was removed. The crude product was distilled under reduced pressure (19 mTorr, 110 ºC ), which yielded 11.25 g (37.1 mmol, 72%) of pure 2-bromo-

3-decylthiophene as a colorless liquid.1H-NMR (400 MHz, CDCl3): 7.18 (d, δ J = 5.6, 1H) 6.79 (d, J = 5.6, 1H) 2.56 (t, J = 7.6, 2 H)

1.62-1.51 (m, 2H) 1.31-1.20 (m, 14H) 0.88 (t, J = 6.8 Hz, 3H). 13C-NMR (CDCl3, 125 MHz): δ 141.66, 127.97, 124.81, 108.80, 32.00, 29.80, 29.72, 29.69, 29.53, 29.45, 29.39, 29.30, 22.78,

14.17.

2,7-Bis(3-decylthiophen-2-yl)-1,6-methano[10]annulene (6.8)

Magnesium (224 mg, 9.22 mmol) was activated by stirring with glass shatters

for 1 hour and 5 mL THF was added. 2-Bromo-3-decylthiophene (2.501 g, 8.25 mmol) in 10 mL THF was added dropwise, the reaction was initiated by

addition of a crystal of iodine, and the mixture was refluxed for three hours. After cooling to room temperature, the Grignard reagent was added dropwise

(via a Teflon cannula) to a mixture of 6.5 (848 mg, 2.83 mmol) and Ni(dppp)Cl2 (12.2 mg, 0.023 mmol) in 20 mL THF/toluene (1:2) and refluxed for 15 hours. The reaction was quenched with

50 mL NH4Cl and 50 mL water and extracted with DCM (3 x 100 mL). The organic layers were washed with water (75 mL) and brine (75 mL), dried over Na2SO4, and filtered. The solvent was

removed and the obtained oil was purified by column chromatography (silica gel, pet. ether 40-60) to give 1.03 g (1.76 mmol, 62%) of the title compound as a yellow oil. 1H NMR (400 MHz, CD2Cl2): 7.35 (d, δ J = 8.7, 2H), 7.29 (d, J = 5.2, 2H), 7.21 (d, J = 9.4, 2H), 7.10 – 7.02 (m, 4H), 2.98 – 2.86 (m, 2H), 2.81 – 2.69 (m, 2H), 1.67 – 1.51 (m, 4H), 1.36 – 1.05

(m, 28H), 0.84 (t, J = 6.9, 6H), -0.09 (s, 2H). 13C NMR (125 MHz, CDCl3): δ 140.89, 136.50, 134.04, 129.68, 129.18, 129.09, 126.75, 124.99, 117.23, 35.17, 31.88, 30.55, 29.56, 29.51, 29.33,

29.30 (multiple signals), 22.67, 14.12. IR (cm-1): 3034, 2922, 2852, 1540, 1464, 1399, 1377, 1290,

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Chapter 6


Calcd for C39H54S2: C, 79.80; H, 9.27; S, 10.93. Found: C, 79.86; H, 9.12; S, 10.81.

2,7-Bis(5-bromo-3-decylthiophen-2-yl)-1,6-methano[10]annulene (6.9)

6.8 (0.840 g, 1.43 mmol) was dissolved in 40 mL THF and cooled with

an ice-salt bath. NBS (0.535 g, 3.95 mmol) in 15 mL THF was added dropwise over 20 minutes. The yellow mixture was stirred for 18 hours

while warming to room temperature and then quenched with 200 mL 2M HCl and extracted with DCM (3 x 200 mL). The organic layers were

washed with water (200 mL) and brine (200 mL), dried over Na2SO4, and filtered. The solvent was removed under reduced pressure and the product was purified by column chromatography

(silica gel, heptane), yielding 0.831 g (1.12 mmol, 78%) of the title compound as a brown oil.1H NMR (400 MHz, CD2Cl2): 7.39 (d, δ J = 8.7, 2H), 7.17 (d, J = 9.5, 2H), 7.07 (t, J = 9.1, 2H),

7.02 (s, 2H), 2.89 – 2.77 (m, 2H), 2.72 – 2.59 (m, 2H), 1.61 – 1.41 (m, 4H), 1.33 – 1.05 (m, 28H), 0.85 (t, J = 6.9, 6H), -0.14 (s, 2H). 13C NMR (50 MHz, CDCl3): 141.65, 138.00, 132.85,δ

131.90, 129.95, 129.20, 127.00, 117.24, 111.66, 34.98, 31.88, 30.35, 29.54, 29.46, 29.29, 29.22, 29.18, 22.67, 14.11. IR (cm-1): 3034, 2920, 2851, 1540, 1524, 1455, 1432, 1376, 1187, 984, 829,

764, 720. HRMS (APCI) calculated for [M+H]+ 745.1930, found 745.1931. Calcd for C39H52Br2S2: C, 62.89; H, 7.04; Br, 21.46; S, 8.61. Found: C, 62.37; H, 6.97; S, 8.51.

Poly(2,7-bis(3-decylthiophen-2-yl)-1,6-methano[10]annulene) (PTM)

6.9 (0.505 g, 0.678 mmol) and bis(pinacolato)diboron (173 mg, 0.680 mmol) were mixed with 23 mL DMF/toluene (1:3) and degassed. K 3PO4

(0.730 g, 3.44 mmol) and Pd(dppf)Cl2.CH2Cl2 (14.6 mg, 0.018 mmol) were added and the mixture was heated for 18 hours at 110 ºC. The solvent was

removed and the resulting solid was dissolved in 30 mL chloroform, precipitated in 400 mL cold methanol, and 5 mL conc. HCl was added. The polymer was

collected by centrifugation and purified by soxhlet extraction using methanol (450 mL, 23 hours), acetone (2 x 450 mL, 23 hours), and chloroform (450 mL, 23 hours). The chloroform

was partially evaporated and the product was precipitated in a vortex of cold methanol and collected by centrifugation. The resulting dark yellow polymer was dried in vacuum, yielding

0.361 g (91%) PTM. 1H NMR (400 MHz, CD2Cl2) 7.47 (bd, δ J = 8.1, 2H), 7.26 (bt, J = 9.0, 2H), 7.17 (bs, 2H), 7.15

– 7.04 (m, 2H), 2.92 (bs, 2H), 2.75 (bs, 2H), 1.62 (bs, 4H), 1.34 – 0.93 (m, 28H), 0.83 (bt, J = 6.0, 6H), -0.05 (d, J = 9.3, 2H). IR (cm-1): 3034, 2920, 2850, 1523, 1455, 1437, 1376, 1253, 1196,

1020, 956, 827, 764, 720. GPC (chloroform): Mn = 6174 g/mol, Mw = 22869 g/mol, PDI = 3.69.

1,5-Bis(3-decylthiophen-2-yl)naphthalene (6.10)

Magnesium (193 mg, 7.98 mmol) was activated by stirring with glass shatters.

2-Bromo-3-decylthiophene (2.251 g, 7.33 mmol) in 5.5 mL ether was added dropwise and the mixture was refluxed several hours. The Grignard reagent was

then added dropwise to a mixture of 1,5-diiodonaphthalene (1.359 g, 3.58 mmol) and Ni(dppp)Cl2 (21 mg, 0.039 mmol) in 26 mL ether/toluene (1:2) and

182


refluxed overnight. The reaction was quenched with 80 mL NH4Cl and extracted with DCM (3 x

100 mL). The organic layers were washed with aq. sat. Na2CO3 (150 mL), brine (150 mL), and water (100 + 200 mL), dried over Na2SO4, and filtered. The solvent was removed and the

obtained oil was purified by column chromatography (silica gel, pet. ether) and recrystallized from isopropanol/methanol (3:1), which yielded 0.957 g (1.67 mmol, 47%) of the title

compound as white powder. 1H NMR (500 MHz, CDCl3): 7.78 (d, δ J = 8.7, 2H), 7.48 – 7.43 (m, 4H), 7.37 (d, J = 5.2, 2H),

7.07 (d, J = 5.2, 2H), 2.38 (t, 4H), 1.52 – 1.43 (m, 4H), 1.27 – 1.12 (m, , 28H), 0.86 (t, J = 7.1, 6H). 13C NMR (125 MHz, CDCl3): 140.92, 135.20, 133.22, 132.21, 129.26, 128.38, 126.71,δ

125.26, 124.37, 31.87, 30.52, 29.53, 29.48, 29.30 (2 signals), 29.19, 28.72, 22.66, 14.11. IR (cm -

1): 3061, 2953, 2922, 2852, 1713, 1590, 1500, 1465, 1393, 1377, 1310, 1227, 1208, 1092, 1069,

1016, 946, 901, 876, 835, 792, 720, 687, 655. HRMS (APCI) calculated for [M+H]+ 573.3583, found 573.3583. Calcd for C38H52S2: C, 79.66; H, 9.15; S, 11.19. Found: C, 79.34; H, 9.04; S,

11.11.

1,5-Bis(5-bromo-3-decylthiophen-2-yl)naphthalene (6.11)

6.10 (0.841 g, 1.47 mmol) was dissolved in 50 mL THF and NBS (0.708

g, 3.95 mmol) in 15 mL THF was added dropwise over 40 minutes. The yellow mixture was stirred overnight and then quenched with 200 mL 2M

HCl and extracted with DCM (3 x 200 mL). The organic layers were washed with brine (200 mL), dried over Na2SO4, and filtered. The solvent

was removed under reduced pressure and the product was recrystallized from isopropanol/methanol (3:1), yielding 0.868 g (1.19 mmol, 81%) of 6.11 as a white powder.1H NMR (500 MHz, CDCl3): 7.90 – 7.76 (m, 2H), 7.51 – 7.40 (m, 4H), 7.03 (s, 2H), 2.31 (bs,δ 4H), 1.50 – 1.40 (m, 4H), 1.32 – 1.01 (m, 28H), 0.87 (t, J = 7.0, 6H). 13C NMR (125 MHz,

CDCl3): 141.70, 136.62, 133.03, 131.17, 131.05, 129.55, 126.90, 125.52, 110.97, 31.87, 30.31,δ 29.52, 29.43, 29.29, 29.23, 29.05, 28.69, 22.66, 14.10. IR (cm -1): 2945, 2921, 2849, 1591, 1504,

1467, 1448, 1393, 1373, 1261, 1209, 1183, 1102, 1069, 1018, 984, 968, 953, 913, 888, 875, 856, 827, 811, 794, 742, 732, 722, 664, 640, 593, 571. HRMS (APCI) calculated for [M+H] +

731.1773, found 731.1772. Calcd for C38H50Br2S2: C, 62.46; H, 6.90; S, 8.78. Found: C, 62.44; H, 6.85; S, 8.76.

Poly(1,5-bis(3-decylthiophen-2-yl)naphthalene) (PTN)

6.11 (0.497 g, 0.68 mmol) and bis(pinacolato)diboron (174 mg, 0.68 mmol) were mixed with 22 mL DMF/ toluene (1:3) and degassed. K 3PO4 (0.750 g,

3.54 mmol) and Pd(dppf)Cl2.CH2Cl2 (13 mg, 0.016 mmol) were added and the mixture was heated to 110 ºC and stirred overnight at this temperature.

Most of the solvent had evaporated and the resulting solid was dissolved in chloroform and precipitated in 400 mL cold methanol. The polymer was collected by

centrifugation and purified by soxhlet extraction using methanol (400 mL, 23 hours), acetone (400 mL, 23 hours), and chloroform (400 mL, 23 hours). The chloroform was partially

evaporated and the product was precipitated in a vortex of cold methanol and collected by centrifugation. The resulting light gray polymer was dried in vacuum, yielding 0.342 g (88%) of

PTN.

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Chapter 6

1H-NMR (400 MHz, CDCl3): 7.95 (bd, J=7.6 Hz, 2H) 7.61-7.46 (b, 4H) 7.20 (b, 2H) 2.39 (b,δ

4H) 1.61-1.42 (b, 4H) 1.32-1.00 (b, 28H) 0.86 (bt, J= 6.8 Hz, 6H). IR (cm -1): 2920, 2850, 1589,1503, 1455, 1395, 1376, 1207, 1180, 1076, 903, 824, 791, 720, 575, 546. GPC (chloroform):

Mn = 10993 g/mol, Mw = 32919 g/mol, PDI = 2.98.

4,7-Bis(3-decylthiophen-2-yl)-2,1,3-benzothiadiazole (6.12)

Magnesium (413 mg, 17.01 mmol) was activated by stirring with glass shatters.

2-Bromo-3-decylthiophene (4.295 g, 14.17 mmol) in 11 mL THF was added dropwise and the mixture was refluxed for 3 hours. After cooling to room

temperature the Grignard reagent was added dropwise to a mixture 4,7-dibromo-2,1,3-benzothiadiazole (1.705 g, 5.80 mmol) and Ni(dppp)Cl2 (48 mg, 0.089 mmol) in

49 mL THF/toluene (4:3) and refluxed overnight. The reaction was quenched with 200 mL NH4Cl and extracted with DCM (3 x 200 mL). The organic layers were washed with aq. sat.

Na2CO3 (250 mL), brine (200 mL), and water (2 x 200 mL), dried over Na2SO4, and filtered. The solvent was removed and obtained oil was purified by column chromatography (silica gel, pet.

ether) to give a mixture of mono- and bis-coupled products. This mixture was treated with more Grignard reagent.

Magnesium (162 mg, 6.68 mmol) was activated by stirring with glass shatters. 2-Bromo-3-decylthiophene (1.68 g, 5.55 mmol) in 4 mL THF was added dropwise and the mixture was

refluxed for 3 hours. After cooling to room temperature the Grignard reagent was added dropwise to Ni(dppp)Cl2 (28 mg, 0.052 mmol) and the mixture of mono- and bis-coupled

products in 29 mL THF/toluene (4:3) and the resulting reaction mixture was refluxed overnight. The reaction was quenched with 100 mL NH4Cl and extracted with DCM (3 x 90 mL). The

organic layers were washed with aq. sat. Na2CO3 (120 mL), brine (120 mL), and water (2 x 120 mL), dried over Na2SO4, and filtered. Solvent were removed and the resulting brown oil was

purified by column chromatography (silica gel, pet. ether/DCM 2:1) and recrystallized from acetonitrile at -35°C, which yielded 0.316 g (0.54 mmol, 9%) of 6.12 as a dark yellow oil at room

temperature.1H NMR (400 MHz, CDCl3): 7.64 (s, 2H), 7.44 (d, δ J = 5.2, 2H), 7.10 (d, J = 5.2, 2H), 2.66 (t, J = 7.7, 4H), 1.68 – 1.57 (m, 4H), 1.33 – 1.00 (m, 28H), 0.86 (t, J = 7.0, 6H). 13C NMR (125 MHz, CDCl3): 154.25, 141.68, 132.14, 129.87, 129.19, 127.43, 125.83, 31.86, 30.71, 29.55, 29.52,δ

29.44, 29.37, 29.34, 29.30, 22.66, 14.10.IR (cm-1): 2953, 2922, 2852, 1577, 1537, 1524, 1465, 1436, 1377, 1336, 1269, 1230, 1094, 876,


4,7-Bis(5-bromo-3-decylthiophen-2-yl)-2,1,3-benzothiadiazole (6.13)

6.12 (0.523 g, 0.90 mmol) was dissolved in 25 ml THF and NBS (0.343 g,

1.93 mmol) in 8 mL THF was added dropwise over 40 minutes. The yellow mixture was stirred overnight and then quenched with 100 mL 2M

HCl and extracted with DCM (3 x 125 mL). The combined organic layers were washed with brine (150 mL) and dried on Na2SO4. The solvent was removed under reduced

pressure to give an orange oil, which contained mono- and bis-brominated products (1:1 ratio) and a trace of starting material. Attempts to purify by column chromatography or

recrystallization were not successful. Therefore, the mixture was dissolved in 25 mL THF and

184


cooled with an ice-salt bath. NBS (0.175 g, 0.98 mmol) in 10 mL THF was added dropwise over

15 minutes and the reaction mixture was stirred for 2 hours and quenched with 120 mL 2M HCl. The mixture was extracted with DCM (3 x 100 mL), washed with brine (150 mL), dried over

Na2SO4, and filtered. The solvent was removed under reduced pressure and the product was purified by column chromatography (silica gel, heptane/DCM 1:1), yielding 0.715 g (0.97

mmol, 108%) of 6.13 as a red oil (that contained traces of solvent).1H NMR (500 MHz, CDCl3): 7.60 (s, 2H), 7.06 (s, 2H), 2.60 (t, δ J = 7.5, 4H), 1.65 – 1.56 (m,

4H), 1.35 – 1.08 (m, 28H), 0.87 (t, J = 7.0, 6H). 13C NMR (125 MHz, CDCl3): 153.89, 142.42,δ 133.51, 131.96, 129.67, 126.59, 113.18, 31.87, 30.52, 29.55, 29.49, 29.39, 29.34, 29.32, 29.30,

22.66, 14.10. IR (cm-1): 2951, 2920, 2850, 1726, 1576, 1525, 1485, 1465, 1431, 1376, 1261, 1185, 1070, 1018, 983, 924, 873, 828, 795, 721, 678. HRMS (APCI) calculated for [M+H] + 739.1242,

found 739.1240. Calcd for C34H46Br2N2S3: C, 55.28; H, 6.28; N, 3.79; S, 13.02. Found: C, 55.91; H, 6.44; N, 3.74; S, 12.98.

Poly(4,7-bis(3-decylthiophen-2-yl)-2,1,3-benzothiadiazole) (PTB)

6.13 (0.666 g, 0.90 mmol) and bis(pinacolato)diboron (158 mg, 0.62 mmol) were mixed with 25 mL DMF/ toluene (1:3) and degassed. K 3PO4 (0.804 g,

3.8 mmol) and Pd(dppf)Cl2.CH2Cl2 (11 mg, 0.013 mmol) were added and the mixture was heated to 120 ºC and stirred overnight at this temperature.

The solvent was removed and the resulting solid was dissolved in chloroform, precipitated in 400 mL cold methanol, and a few drops of conc. HCl were added. The polymer was collected by

centrifugation and purified by soxhlet extraction using methanol (400 mL, 23 hours), acetone (2 x 400 mL, 23 hours each), and chloroform (400 mL, 23 hours). The chloroform was partially

evaporated and the product was precipitated in a vortex of cold methanol and collected by centrifugation. The resulting dark red polymer was dried in vacuum, yielding 0.233 g (44%) of

PTB. 1H-NMR (400 MHz, CDCl3): 7.74-7.61 (m, 2H), 7.07 (s, 2H), 2.76-2.54 (m, 4H), 1.73-1.62 (b,δ

4H), 1.35-0.92 (b, 28H), 0.85 (bt, J= 6.1 Hz, 6H). IR (cm -1): 2952, 2918, 2849, 1569, 1533, 1483, 1465, 1433, 1376, 1338, 1262, 1184, 1026, 874, 844, 822, 720, 700, 684. GPC (chloroform): M n

= 2941 g/mol, Mw = 4679g/mol, PDI = 1.58.

185

Chapter 6


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186


27. W. Klug, PhD Thesis "Substitutionsprodukte des 1,6-Methano-[10]annulens" Universität Köln, 1972.

28. The simple model described in Section 4.5.2 predicts (based on length and calculated HOMO level) that the conductance values of both 6.6 and 6.7 will be between those of molecular wires 4.2 (OPE3) and 4.4 (1,4-disubstituted naphthalene-wire).

29. F. Brouwer, J. Alma, H. Valkenier, T.P. Voortman, J. Hillebrand, R.C. Chiechi, J.C. Hummelen, J. Mater. Chem. 2011, 21, 1582-1592.

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Chapter 6

188

Chapter 7The Matrix Approach Revisited

In this concluding chapter we summarize and discuss the results from the Matrix Approach, in which the conductance of several series of molecular wires was investigated by five methods. We describe the trends in the molecular conductance that we found for these series and how the junction geometry influences these trends and the absolute conductance values. Additionally, we compare the results from conductance measurements on monothiolated and dithiolated molecular wires in different junctions. We finish this chapter with a discussion on the consequences of the results of our conductance studies.

189

Chapter 7

7.1 Results from the Matrix ApproachIn Chapter 1.5 we have introduced our Matrix Approach on molecular

conductance. We have designed and synthesized five series of molecular wires

(described in the Chapters 2, 3, 4, and 6), that all have their rigid oligo(1,4-

phenylene ethynylene) (OPE)-based structure and thiolate anchoring groups in

common. We varied the length, HOMO-LUMO gap and conjugation pattern of

these wires by changing their central unit, to study the influence of these properties

on the conductance. In collaborations with different groups, we have used several

methods to study the conductance of these wires. These are single molecule

methods like Scanning Tunneling Microscopy Break Junctions (STM-BJ) and

Mechanically Controllable Break Junctions (MCBJ), Conductive Probe Atomic

Force Microscopy (CP-AFM, by which about a hundred molecules are contacted),

and much larger junctions formed with the eutectic alloy of gallium and indium as

top contact (EGaIn) as well as Large Area Molecular Junction (LAMJ) devices.

Before we present the overview of the results obtained by this Matrix Approach

and the conclusions in Section 7.1.3, we present the results from CP-AFM and

MCBJ studies on the length dependence of the conductance OPEs in the next two

sections.

7.1.1 OPE Length Dependence of the Conductance in CP-AFM junctions1

We have grown SAMs of molecular wires OPE2-4 according to the triethylamine

deprotection procedure described in Chapter 3 and investigated the charge

transport through these SAMs upon contacting with a gold-coated contact-mode

AFM tip as described in Chapter 5.3. I-V curves were measured and conductances

were obtained from linear fits of the data between -100 mV and 100 mV.

Histograms from these conductances are given in Figure 7.1a. We obtained a

conductance value for each OPE from a Gaussian fit of the largest peaks in the

histogram. A semilogarithmic plot of these values versus the molecular length

shows that the conductance (G) decays exponentially with the length (L),

according G = A e· - Lβ with exponential decay parameter β = 0.37 Å-1 (Figure 7.1b).

This is in very good agreement with the value β = 0.33 Å-1 that we found for

OPE2-4 in the STM Break-Junction method (Chapter 4) and with the value

reported for electrochemical charge transfer experiments through OPE bridges

190

The Matrix Approach Revisited

(0.36 Å-1),2 though larger than the values previously reported for CP-AFM

experiments with Ti/Pt tips (0.21 Å-1)3 and on OPEs with amine anchoring groups

(0.20 Å-1).4

7.1.2 OPE Length Dependence of the Conductance in MCBJs5

The conductance of OPE2-4 was investigated by Wenjing Hong, University of

Bern, with notched gold wire-based MCBJs. The wire was broken in the presence

of a 0.1 mM solution of bisacetyl protected OPE dithiols in mesitylene/THF (4:1)

on air. The break junction was repeatedly opened and closed, while measuring

conductance-distance traces. The resulting histograms are depicted in Figure 7.2a

and the positions of the peaks are very close to those found in the STM-BJ

experiments (see also Table 7.1). The fit of these conductance values gave an

exponential decay parameter β = 0.34 Å-1, being very close to the values found by

STM-BJ (0.33 Å-1) and CP-AFM (0.37 Å-1).

191

Figure 7.1 a. Conductance histograms of OPE2-4 obtained from CP-AFM measurements. b. Fit of the exponential decay of the conductance of OPE2-4 as function of the molecular length with β = 0.37 Å-1. (Leiden, note 1)

Chapter 7

I-V curves were recorded while slowly opening and closing the junction with

OPE3.6 The mean curve from the statistical analysis is plotted in Figure 7.2b,

together with a few individual I-V curves. The slope of the linear regime (-500 mV

to 500 mV) was determined for all individual I-V curves and a histogram was

constructed from the obtained conductance values (Figure 7.2c, black), which has

a shape similar to the histogram from the conductance-distance traces (Figure 7.2c,

green). This confirms that the conductance values that are obtained from current-

distance traces in break junction experiments (STM-BJ and MCBJ) can be

compared directly to conductance values determined from I-V curves (as in this

MCBJ experiment, but also in CP-AFM experiments). This supports the good

agreement found between the conductance values obtained from CP-AFM

measurements and from break junction methods (Figure 7.3).

192

Figure 7.2 Results from conductance measurements in notched gold wire-based mechanically controllable break junctions (ambient) at a bias of 100 mV. a. Histograms from conductance-distance traces of OPE2-4. b. I-V curves of OPE3. c. Conductance histogram of OPE3 obtained from a linear fit (-0.5 to 0.5 V) of the slope of 16575 individual I-V curves (black), which shows a peak at the same position as the conductance histogram that was obtained from 1600 conductance-distance traces (green). (Bern, note 5)


7.1.3 The Matrix Approach: Summary and Conclusions

The Matrix Approach offers the advantage that all molecules have an identical

design (an OPE-type core and two thiolate anchoring groups) and that all

molecules, of which the conductance was measured in different laboratories, were

synthesized in the same laboratory according to a general strategy. Furthermore,

the formation of unreproducible or ill-defined self-assembled monolayers (SAMs)

was excluded by an in depth investigation of the self-assembly (Chapter 3).

The results of these investigations are summarized in Table 7.1 and Figure 7.3. To

estimate the conductance per molecule we assumed that around a hundred

molecules are contacted in the CP-AFM junction7 and that the packing density of

the molecular wires in the SAMs is 4 10· 18/m2 (or: 4 10· 6/ mμ 2), corresponding to an

area of 25 Å2 per molecule.8

Not all molecular wires were studied by all possible methods, mainly due to large

time consumption and/or high costs of the measurements or practical problems

like the high or low current limits of the measurements or problems with the

experimental protocols to apply the molecules in the junction. Furthermore, not all

methods are suitable to study all series. Molecular wires 4.4 and 4.5, for instance,

are expected to have a packing density that deviates substantially from that of

OPE3,9 which obfuscates the comparison of conductance measurements on

densely packed SAMs of these molecules.

Comparison of the Methods for Conductance Measurements

When comparing the five different junctions used to study molecular conductance,

we find a very good agreement between the results from single molecule STM-BJ

and MCBJ experiments and from the measurements on SAMs by CP-AFM

(Figure 7.3, upper part). The trends found are identical, as are the absolute

conductance per molecule values, based on the assumption that we contact a

hundred molecules in a CP-AFM junction. These three methods have in common

that gold-molecule-gold junctions are formed, which is a relatively well-defined

system. STM-BJ experiments have the advantages to be very fast and not to require

densely packed SAMs. MCBJs are more stable compared to STM-BJs, which

allows to measure I-V curves. An additional advantage is that only a few molecules

need to be present on the gold surface of the junction area. In contrast, CP-AFM

studies require densely packed SAMs. Since many molecules are measured in

parallel, the currents through these junctions are larger and less specialized

193

Chapter 7

electronics can be used. Furthermore, the large number of molecules and the less

dynamic character of the junction cancel out small differences in binding

geometry. The good agreement between the results from different junctions and

different labs shows that these three gold-molecule-gold methods are highly

suitable to study the influence of molecular structure on the conductance.

Table 7.1 Summary of the results from the conductance measurements by various methods.

Structure Name STM-BJ

MCBJ CP-AFM

EGaIn LAMJ Modela

G (nS)

G (nS)

G (nS)

G (nS/μm2)

G (nS/μm2)

G (nS)

OPE24.1 114 117 10428 - 11749b 114

OPE34.2 13.9 10.0 841 - 5012b 11

OPE44.3 1.22 1.1 63 - 4266b 1.1

G=A⋅e−⋅L β (Å-1) 0.33 0.34 0.37 - 0.07-0.15d

4.4 20.8 - - - - 15

4.5 36.4 - - - - 43

4.6 4.12 - - - - 5.8

26AC2.6/4.7 3.61 1.95 221 108e 15286c 4.1

AQ2.1 - 0.008 6.9 0.69e 5750c 1.1

H2AC2.7 - 0.04 32 1.9e 2512c 2.3

a. Predicted values for tunneling through a rectangular barrier, based on the length and HOMO level (see Chapter 4.5). The results from STM-BJ experiments are used to parameterize this model.

b. Devices were fabricated at MiPlaza in Eindhoven, according ref. 1010 and the resistance was determined at 0.5 V.c. Devices were fabricated at the University of Groningen (see Section 5.9.2) and the resistance was determined

at 0.1 V.d. The series [benzenedithiol-OPE2-OPE3] gave a β value of 0.15 Å-1, whereas the series [OPE2-OPE3-OPE4]

gave a value of 0.07 Åβ -1. e. Determined from a Gaussian fit of the current density histogram at 0.1 V.* All conductance measurements are performed in collaborations, as listed in Chapter 1.5.

194


The molecular conductance values obtained from LAMJ and EGaIn experiments

are four to five orders of magnitude lower (Figure 7.3, gray background). We

might have overestimated the packing density of the molecules or the contact area

(due to trenches in the gold surface, in which the molecules are not contacted by

the top electrode, or due to defects in the SAM), though these parameters will

count for one to two orders of magnitude at most. A better explanation for these

orders of magnitude lower conductances is found in the top contacts. The

resistance of the ~90 nm thick PEDOT:PSS interlayer and its interface with the

SAM contribute (rSAM/PEDOT:PSS) to the total resistance of the LAMJ (RLAMJ) in a

factorized way (RLAMJ = 12.9 k rΩ · Au-S r· SAM r· SAM/PEDOT:PSS).7 In EGaIn junctions the

SAM is separated from the metallic GaIn top contact by a thin layer of Ga2O3 (~1

nm), which most likely acts as an additional tunneling barrier. These more

195

Figure 7.3 Results of the Matrix Approach: Plot of the low bias conductance per molecule versus the length of the molecular wires for wires OPE2-4 (green), 4.4 (orange), 4.5 (purple), 4.6 (dark blue), 4.7=26AC (blue), AQ (red), H2AC (black). The results from different methods are plotted with different symbols. Exponential fits of the STM-BJ data and LAMJ data on OPE2-4 are plotted as green lines. The upper part of this plot contains all values measured in junctions with two gold contacts (white background). The lower part of this plot contains the values obtained from junctions with a top contact other than gold (gray background).

Chapter 7

complex top contacts of LAMJs and EGaIn junctions not only give rise to lower

absolute conductance values, but also to less strong length dependence of the

conductance (i. e., lower values for exponential decay parameter β). A difference

between these two methods is the large influence of the conjugation pattern on the

conductance found in EGaIn junctions, compared to the less pronounced trend in

LAMJs.

EGaIn junctions, LAMJs and junctions formed by CP-AFM have the requirement

of high quality densely packed SAMs in common. An advantage of EGaIn

junctions and LAMJs is that these junctions are formed over areas of around 80-

8000 mμ 2, which provides the possibility to study the influence of the quality of

the SAM on the charge transport properties, as is possible with mercury junctions.11 In Chapter 3.6 we have shown that the conditions used for the formation of

SAMs determine the resistance of LAMJs up to three orders of magnitude. When

using EGaIn as a top contact, the yield of good junctions decreases dramatically

when SAMs are less densely packed, leading to a large percentage of shorted

junctions.12

The trends found in the absolute conductance values upon comparing different

types of junctions with π-conjugated wires are in good agreement with the trends

described for alkanethiol junctions formed by different methods13: we found the

highest conductance values (or lowest resistance) when the molecules had two

chemisorbed contacts (e.g., thiolate-gold bonds in STM-BJ, MCBJ, CP-AFM),

lower conductance values for molecules with one chemisorbed contact (see Section

7.2.1), and the lowest conductance values in the presence of a resistive interlayer

(PEDOT:PSS in LAMJs or Ga2O3 in EGaIn junctions). However, in contrast to

junctions with alkanethiols, the exponential decay factor was influenced by theβ

resistive interlayer as well.

Trends in the Relationship between Molecular Conductance and Structure

Figure 7.3 shows a strong dependence of conductance on the molecular length, as

described for the STM-BJ results in Chapter 4 and confirmed with the results from

CP-AFM and MCBJ measurements (see next sections). The conductance values

(G) from these experiments decay exponentially as function of the length (L),

according to the description for tunneling through a rectangular barrier: G = A e· - Lβ ,

with exponential decay parameter β varying from 0.33-0.37 Å-1. The conductance

values from linear conjugated anthracene- and naphthalene-based wires are found

196


to be very close to the fit belonging to the length dependence of OPE2-4.

Naphthalene- and anthracene-based wires 4.4 and 4.5 were found to have 1.5 and

2.6 times larger conductance values than OPE3. We attributed this to the relatively

high energy of the HOMO levels of these compounds, which decreases the offset

between the Fermi energy of the gold electrode and the HOMO, decreasing the

height of the tunneling barrier. In the last column of Table 7.1 we listed the values

obtained from a highly simplified model for molecular conductance as tunneling

through a rectangular barrier in which the width of the barrier is determined by the

length of the molecule and the height of the barrier by the offset between the

HOMO level and the Fermi energy of gold.14 Alternative explanations for the

relatively large conductance values for these anthracene and naphthalene wires,

like their relatively small HOMO-LUMO gap or the gain in aromaticity upon

formation of quinoid structures,15,16 can be traced back to the high energy of the

HOMO levels.

Strong deviations from the length dependence trend were found for the cross-

conjugated anthraquinone wire (AQ, red) and the dihydroanthracene wire with

broken conjugation (H2AC, black). Their relatively low HOMO levels can only

account for a factor two to four reduced conductance and not for the about two

orders of magnitude that we found experimentally. We explained the low

conductance of the broken-conjugated wires by the lower electronic coupling

between their two π-conjugated parts. Also in the cross-conjugated wires the

electronic coupling is lower than in linear conjugated wires. Destructive quantum

interference was predicted for this cross-conjugated AQ wires. This dramatically

reduces their conductance at small bias voltages (see Chapter 5).

197

Chapter 7

7.2 A Comparison of the Conductance of Monothiolated and Dithiolated OPE3In the previous section we have discussed the results from conductance studies on

molecular wires with two thiol-based anchoring groups. In this Section we will

focus on the comparison of the results from conductance measurements on

monothiolated OPE3 (monoS-OPE3) and dithiolated OPE3 (diS-OPE3), of which

the synthesis and formation of self-assembled monolayers were described in

Chapter 3.

7.2.1 Comparison of OPE3 monothiol and dithiol in CP-AFM junctions1

As we described in Section 7.1, the CP-AFM method does provide relatively well-

defined gold-molecule-gold junctions. In these junctions, one thiolate anchoring

group is chemisorbed at the gold surface of the substrate, providing a good

coupling to the bottom contact. The nature of the top contact could vary. When a

SAM of dithiols is contacted, the thiol groups on top of the SAM (about half of

198

Figure 7.5 Averaged I-V curves of monoS-OPE3 (black) and diS-OPE3 (red) as measured by CP-AFM. (Leiden, note 1)

Figure 7.4 Chemical structures of diS-OPE3 and monoS-OPE3.


which bears an acetyl protecting group) will chemisorb to the gold-coated AFM tip17 and form a symmetric gold-molecule-gold junction. In contrast, when the AFM

tip contacts a SAM of monothiols, then only a physical contact can be formed due

to the force on the tip.

We have investigated the conductance of SAMs of diS-OPE3 and monoS-OPE3

and plotted the averaged I-V curves in Figure 7.5. We found the I-V curve of diS-

OPE3 to be symmetric, which indicates that indeed a chemisorbed contact

between the SAM and gold coated AFM tip was established. In contrast, the I-V

curve of monoS-OPE3 is asymmetric: the current at -1.2 V is 2.5 times larger than

the current at +1.2 V. Furthermore, the conductance of diS-OPE3 at low bias

voltages (±100 mV) is around three times larger than the conductance of monoS-

OPE3, as expected for a junction with one chemisorbed and one physisorbed

contact.

7.2.2 Comparison of OPE3 monothiol and dithiol in MCBJs18

The conductance of diS-OPE3 and monoS-OPE3 was studied in lithographically

defined break junctions in vacuum at Delft University.18 The molecules were

applied by immersion of the break junction substrates overnight in solutions of the

acetyl-protected molecules in THF (under nitrogen), after which the samples were

rinsed, dried and mounted in the setup.19 Current-distance traces were measured

upon opening of the break junctions and histograms were constructed without any

data selection. The histogram of diS-OPE3 as shown in Figure 7.6 shows a broad

molecular feature around 10-4 G0, which is not present in the histogram of clean

199

Figure 7.6 Histograms of the conductance-distance traces measured for diS-OPE3 (blue, 500 traces) and clean gold (red, 2100 traces) in lithographically defined mechanically controllable break junctions in vacuum at a bias of 50 mV and a stretching speed of 1 nm/s. (Delft/Leiden, note 18)

Chapter 7

gold. A clear feature is observed at 7 10· -5 G0 (~5 nS) and a shoulder could be

present at 2 10· -4 G0 (~15 nS), though no firm conclusions can be made on that.

These values are close to the values obtained from STM-BJ measurements (14 nS)

and ambient MCBJ measurements (10 nS) and the values reported in the literature

(13 nS,20 9 nS,21 10 nS,22 4 nS23).

Two dimensional histograms24 were obtained for monoS-OPE3 and diS-OPE3

(Figure 7.7). The 2D-histogram of diS-OPE3 shows plateau-like features around

10-4 G0, which have formed the peak in the histogram in Figure 7.6. In contrast, no

plateau-like feature are observed for monoS-OPE3, indicating that no molecular

Au-molecule-Au junctions are formed with this asymmetric molecule, as expected

for a molecule with only one anchoring group.

7.2.3 Comparison of OPE3 monothiol and dithiol in STM-BJs25

In the discussed MCBJ experiments in vacuum, no conductance was found for

monoS-OPE3. However, conductance peaks around 6·10-6 G0 (0.5 nS) were

recently recorded in MCBJ experiments in a liquid environment26 and ambient

STM-BJ experiments27 on this monothiol and on a monoS-OPE3 with two

methoxy groups on the central phenyl ring. This low conductance feature was

attributed to π-π interactions28 between two monoS-OPE molecules, each of which

is bound to one of the electrodes (Figure 7.8a). A surprisingly large conductance

200

Figure 7.7 2D Histograms of the conductance-distance traces measured for diS-OPE3 (a, 500 traces) and monoS-OPE3 (b, 1600 traces) in lithographically defined mechanically controllable break junctions in vacuum at a bias of 50 mV and a stretching speed of 1 nm/s. (Delft/Leiden, note 18)


through π-π stacked conjugated units was previously reported by Seferos et al. for

an OPV-type molecular wire of which the two π-conjugated parts were covalently

linked in the π-π stacked configuration by a [2,2]paracyclophane unit (Figure

7.8b).29

To investigate if the reported low conductance feature26,27 indeed originates from π-

π stacking, this interaction was tuned by varying the solvents in the liquid cell of

the STM-BJ setup. These experiments were performed by Veerabhadrarao

Kaliginedi at the University of Bern. The MCBJ experiments from the

Schönenberger group (University of Basel) were performed in mesitylene/THF

(4:1),26 also used in the STM-BJ experiments in Chapter 4. THF was used as a

good solvent for the OPE compounds and mesitylene is a high boiling and apolar

solvent, which minimizes leakage currents. However, mesitylene is an aromatic

solvent which has π-π interactions with the OPE molecules. Better π-π stacking of

the monoS-OPE3 molecules in the junctions was therefore expected in a non

aromatic solvent like decane. The conductance measurements of diS-OPE3 in

decane/THF (5:1) gave a conductance histogram with a large high conductance

peak (~19 nS) and a low conductance peak (~0.8 nS, Figure 7.9a), similar to the

measurements in mesitylene/THF (Chapter 4). MonoS-OPE3 was measured in

both solvent mixtures. A clear peak in the conductance histogram (without data

201

Figure 7.9 Histograms from all conductance-distance traces measured in STM break junctions at a bias of 100 mV for a. diS-OPE3, dissolved in decane/THF (5:1), b. monoS-OPE3, dissolved in decane/THF (5:1), and c. monoS-OPE3, dissolved in mesitylene/THF (5:1). (Bern, note 25)

Figure 7.8 a. Schematic of the π-π stacking of two monoS-OPE3 molecules in a junction (the exact geometry of this stacking phenomenon is unknown). b. The covalently bound π-π stacked wire of Seferos et al.29

Chapter 7

selection) was obtained in decane/THF (Figure 7.9b), whereas the features in the

histogram from the measurements in mesitylene/THF are much broader (Figure

7.9c). Similar trends were found for the monoS-analogues of naphthalene wire 4.4

and anthracene wire 4.5.12 This is a compelling indication for enhanced π-π

stacking in the junctions in decane, as predicted.

The strong conductance peak in the histogram of monoS-OPE3 measured in

decane is located at 10-5 G0 (~0.8 nS), which is close to the previously reported

values. This value is very close to the G2 (or: Low G) value of diS-OPE3, which

we attributed to a different contact geometry. Hence, although the arguments for a

low conductance signal due to an adatom-top or adatom-adatom configuration as

presented in Chapter 4.7 are also strong, we cannot exclude a contribution of π-π

stacking to this peak.27

We note that the formation of junctions upon π-π stacking of monothiolated π-

conjugated wires is more likely to happen in the presence of a solution of these

monothiols (as in the STM-BJ experiments) than in a junction in vacuum, where

less molecules are present on the gold surface (Section 7.2.2). In such a junction in

vacuum, the chance to observe a conductance signal from π-π stacked monothiols

is strongly influenced by the number of molecules absorbed on the junction and

their distance from the exact position where the Au-Au junction breaks, which

could vary from experiment to experiment. From the 2D histogram shown in

Figure 7.7 we cannot conclude that the formation of junctions by π-π stacked

monothiols is impossible in MCBJs in vacuum, however in this experiment no

peaks or plateaus due to π-π stacking were observed.

202


7.3 Perspectives of Molecular Electronics and π-LogicHaving investigated and discussed how both the structure of molecules and the

junction geometry influence molecular conductance, we conclude this thesis with a

discussion regarding the consequences of these results on the perspectives of

molecular circuits and π-logic30 (see Chapter 1.3). Even though the field of

molecular electronics has expanded tremendously during the past five to ten years,

as have the experimental possibilities, contacting molecules selectively with more

than two electrodes (as required for π-logic) is a remaining challenge. Constructing

electronic circuits from molecules only has still a long way to go. Since the

understanding of molecular electronics has increased, we will evaluate our results

on π-conjugated molecules from a more fundamental perspective.

The results presented in this thesis are mainly grouped in two categories: linear

conjugated molecular wires (Figure 7.10a) and π-conjugated wires with an

alternative conjugation pattern (i.e., cross-conjugation and broken conjugation).

Figure 7.10b shows the cross-conjugated anthraquinone-based wire, which has the

potential to switch to a linear conjugated state, as described in Chapter 2. We note

that this anthraquinone wire is doubly cross-conjugated: the bold pathway in

Figure 7.10b has three subsequent single bonds and alternative pathways through

this molecule for instance include two times two subsequent single bonds. We

assume this double cross-conjugation not to influence our conclusions when

comparing linear conjugated and cross-conjugated molecular wires.

203

Figure 7.10 Schematic of the linear conjugated anthracene wire (a.) and the cross-conjugated anthraquinone wire (b.) attached to gold electrodes.

Chapter 7

Linear Conjugated Molecular Wires

We found that the molecular conductance of linear conjugated molecules is mainly

determined by their length. The only thing that distinguishes linear conjugated

molecules from alkanethiols is that their length dependence is less strong (lower β

values). Properties such as the energetic position of the HOMO level and the

HOMO-LUMO gap have only a relatively minor influence on the conductance.

However, here we should comment that these conductance studies mainly consider

the low bias conductance (~100 mV), where at higher voltages the conductance of

π-conjugated molecular wires increases significantly.31 Charge transport through

the discussed electrode-molecule-electrode junctions is best described as non-

resonant tunneling. However, a transition from tunneling to a hopping mechanism

has been reported for longer π-conjugated molecules (~4 nm for oligoarylene-

imides32 and ~2.5 nm for OPEs33). The decrease of the conductance with length is

less strong (linear instead of exponential) when the hopping mechanism takes over,

though the absolute conductance values are lower compared to tunneling. Further

influences of molecular structure on hopping-dominated transport through longer

molecular wires are to be explored.

Cross-conjugated Molecular Wires

We have investigated the influence of the conjugation pattern on the molecular

conductance by comparing the molecules depicted in Figure 7.10 and found

support for the assumption made in the development of the π-logic concept30 that

the cross-conjugated molecule has a about fifty times lower conductance than the

linear conjugated molecule (of nearly identical length). This difference is better

explained by quantum interference effects of the wave functions of transmitted

electrons than by hindered delocalization of charges in cross-conjugated pathways

(for in a real non-resonant tunneling model, no charges reside on the molecule in

the tunnel junction). Quantum interference effects are generally found around the

Fermi energy for cross-conjugated molecules,34,35 resulting in lower conductances.

However, they are not necessarily limited to this class of compounds and have also

been predicted for linear conjugated molecules with nitro-substituents,36,37 with

alkene substituents,38 and for molecules with fluorenone and related groups

incorporated.39 Quantum interference has the potential to tune the conductance

over several orders of magnitude, making it highly suitable for conductance

switching, and ultimately, chemical computing. Although we found strong

indications for quantum interference in our experimental results, experimental

204


proof for quantum interference is still to be observed.

In the molecules that were designed as logic gates in the π-logic concept (Chapter

1.3), the conjugation pattern of pathways between terminals was compared instead

of the conjugation pattern of rod-shaped wires (Chapter 5). In these larger π-

conjugated structures, all possible pathways between the terminals can be

considered as transmission channels for the conductance. During the development

of π-logic, linear conjugated pathways were considered to have a transmission of

"1" and cross-conjugated pathways to have "0" transmission. However, the (only

available) linear conjugated pathway is often much longer than the shortest cross-

conjugated pathway. When the transmission through this (short) cross-conjugated

pathway is reduced seriously by quantum interference, its conductance will be

dominated by the -system.σ 40 It is unlikely that the transmission through a short -σpathway is indeed "0" compared to the transmission through significantly longer

linear conjugated pathway, since the difference in conductance for molecules of

(nearly) identical length was only about two orders of magnitude. Transport

calculations would give more insights into the perspectives of π-logic.

205

Chapter 7


1. CP-AFM measurements were performed by Constant Guédon and Sense Jan van der Molen at Leiden Univerity.

2. S. Creager, C.J. Yu, C. Bamdad, S. O'Connor, T. MacLean, E. Lam, Y. Chong, G.T. Olsen, J. Luo, M. Gozin, J.F. Kayyem, J. Am. Chem. Soc. 1999, 121, 1059-1064.



5. Ambient MCBJ measurements were performed by Wenjing Hong, in the group of Thomas Wandlowski at the Univerity of Bern.

6. E. Lörtscher, H.B. Weber, H. Riel, Phys. Rev. Lett. 2007, 98, 176807.

7. A. Salomon, D. Cahen, S. Lindsay, J. Tomfohr, V.B. Engelkes, C.D. Frisbie, Adv. Mater. 2003, 15, 1881-1890.

8. Yang, Y. Qian, C. Engtrakul, L. Sita, G. Liu, J.Phys.Chem.B 2000, 104, 9059-9062.

9. D. Nilsson, S. Watcharinyanon, M. Eng, L. Li, E. Moons, L.S.O. Johansson, M. Zharnikov, A. Shaporenko, B. Albinsson, J. Martensson, Langmuir 2007, 23, 6170-6181.



12. All junctions shorted when triethylamine was omitted from the solutions used for the formation of the SAMs.


14. J.R. Quinn, F.W. Foss, L. Venkataraman, R. Breslow, J. Am. Chem. Soc. 2007, 129, 12376-12377.

15. R. Breslow, F.W. Foss, J. Phys.: Condens. Matter 2008, 20, 374104.

16. A.M. Fraind, J.D. Tovar, J. Phys. Chem. B 2010, 114, 3104-3116.

17. H. Skulason, C.D. Frisbie, J. Am. Chem. Soc. 2000, 122, 9750-9760.

18. UHV MCBJ measurements were performed by Christian Martin and Roel Smit in the groups of prof. Herre van der Zant at Delft University of Technology and prof. Jan van Ruitenbeek at Leiden University.

19. C.A. Martin, R.H.M. Smit, R. van Egmond, H.S.J. van der Zant, J.M. van Ruitenbeek, manuscript in preparation; R.H.M. Smit et al., manuscript in preparation.

20. X. Xiao, L.A. Nagahara, A.M. Rawlett, N. Tao, J. Am. Chem. Soc. 2005, 127, 9235-9240.

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30. M. H. van der Veen, PhD Thesis "π-Logic" University of Groningen, 2006.

31. E. Lörtscher, M. Elbing, M. Tschudy, C. von Hänisch, H.B. Weber, M. Mayor, H. Riel, ChemPhysChem 2008, 9, 2252-2258.

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207


Publications

Publications

Synthesis and Properties of an Anthraquinone-Based Redox Switch for Molecular ElectronicsE. H. van Dijk, D. J. T. Myles, M. H. van der Veen, J. C. Hummelen, Org. Lett. 2006, 8, 2333-2336.

Foldamers at InterfacesJ. van Esch, H. Valkenier, S. Hartwig, S. Hecht, Foldamers: Structure, Properties, and Applications (Eds.: S. Hecht, I. Huc), Wiley-VCH, Weinheim, 2007, 403-426.

Using bis(pinacolato)diboron to improve the quality of regioregular conjugated co-polymersF. Brouwer, J. Alma, H. Valkenier, T. P. Voortman, J. Hillebrand, R. C. Chiechi, J. C. Hummelen, J. Mater. Chem. 2011, 21, 1582-1592.

Controlling the interparticle distance in a 2D molecule-nanoparticle networkC. M. Guédon, J. Zonneveld, H. Valkenier, J. C. Hummelen, S. J. van der Molen, Nanotechnology, 2011, 22, 125205.

The Formation of High Quality Self-Assembled Monolayers of Conjugated Dithiols on Gold: Base Matters H. Valkenier, E. H. Huisman, P. A. van Hal, D. M. de Leeuw, R. C. Chiechi, J. C. Hummelen, J. Am. Chem. Soc. 2011, 133, 4930-4939.

Effect of molecular length and molecular structure on the conductance of OPE type molecular wires: An STM break junction approachV. Kaliginedi, H. Valkenier, V. M. García-Suárez, P. Moreno-García, W. Hong, P. Buiter, J. L. H. Otten, J. C. Hummelen, C. Lambert, Th. Wandlowski, manuscript in preparation.

Evidence for Quantum Interference in SAMs of Arylethynylene Thiolates in Tunneling Junctions with Eutectic Ga-In (EGaIn) Top-ContactsD. Fracasso, H. Valkenier, J. C. Hummelen, G. Solomon, R. C. Chiechi, J. Am. Chem. Soc. 2011, in press.

Observation of Quantum Interference in Molecular Charge TransportC. M. Guédon, H. Valkenier, T. Markussen, K. S. Thygesen, J. C. Hummelen, S. J. van der Molen, submitted.

The influence of the conjugation pattern on charge transport in Au-molecule-Au junctionsH. Valkenier, C. M. Guédon, T. Markussen, K. S. Thygesen, S. J. van der Molen, J. C. Hummelen, manuscript in preparation.

209

Summary

SummaryThis thesis describes how the molecular structure determines the conductance of

rigid π-conjugated molecules: molecular wires. We developed a library of

molecular wires, synthesized by a general scheme, and studied molecular

conductance by the "Matrix Approach". In that, we study trends in the molecular

conductance of several series of molecular wires in five different junction geometries.

The resulting matrix allows to compare these trends for different junctions and

separate technical influences from the influence of molecular structure on

conductance.

Determining the molecular conductance is a first step. Controlling molecular

conductance by means of switching is an important requirement on the road

towards functional molecular electronic devices. In Chapter 2 we present an

anthraquinone-based redox-switch. This molecule is cross-conjugated in its stable

state, and turns linear conjugated upon (electro)chemical reduction. Oxidation of

the linear conjugated state returns it to the cross-conjugated state. This cross-

conjugated state is expected to have a lower conductance compared to the linear

conjugated state, due to the reduced electronic coupling in cross-conjugated π-

systems. Reduction and oxidation are, in principle, electronic tools that allow fast

and complete switching of the molecular switch between these high and low

211

Figure 1 The Matrix Approach, in which the trends in molecular conductance of several series of molecular wires are studied in different junction geometries.

Summary

conductance states.

Before measuring the conductance of our molecular wires and switches, we

describe in Chapter 3 the formation of contacts between the molecules and the

electrodes. The molecular wires discussed in this thesis have thiol groups on both

ends of the molecular wire, to anchor the molecules to gold electrodes via thiolate-

gold bonds. These thiol anchoring groups are protected with acetyl groups, to

prevent the conjugated thiols from degradation (by oxidation on air). When these

π-conjugated dithioacetates bind to gold, the acetyl groups disappear and the

molecules form a self-assembled monolayer (SAM). However, this SAM did not

have the maximum packing density. Densely-packed and high-quality SAMs were

obtained when a small fraction of the thioacetate groups was deprotected to form

thiolate anions. We have shown in Chapter 3 that this can be realized upon

immersion of a gold surface for two days in a solution of π-conjugated

dithioacetates, to which ~10 % triethylamine was added. Alternatively,

dithioacetates can be deprotected with a stronger base or nucleophile as we

illustrated with tetrabutylammonium hydroxide. Addition of four equivalents

resulted in solutions of molecules with two thiolate anions, which formed

monolayers of molecules laying flat on the gold surface. The addition of one to

two equivalents tetrabutylammonium hydroxide as deprotecting agent allowed the

formation of SAMs in less than one hour. However, these SAMs have more defects

than those formed with triethylamine and have tetrabutylammonium counter ions

incorporated. The conditions used for the formation of SAMs have a major

influence on charge transport properties of the SAMs, as we have shown in Large

Area Molecular Junction (LAMJ) devices.

Chapter 4 presents three series of linear conjugated molecular wires. The trends in

the conductance of these wires was investigated by the Wandlowski group with the

Scanning Tunneling Microscopy Break Junction (STM-BJ) method. The

conductance of the molecular wires was found to be mainly determined by the

length of the wires. Wires with a smaller HOMO-LUMO gap (or higher HOMO

level) showed a higher conductance, although the influence of length dominates

the charge transport, which is described by a non-resonant tunneling model.

Transport calculations confirmed the experimental trends.

Chapter 5 discusses the influence of the π-conjugation pattern on the charge

transport properties of molecular wires. After analysis of the SAMs grown from

this series of molecular wires, the results from conductance studies by several

212

Summary

methods (all performed in collaborations with different groups) are discussed.

Electrical measurements through SAMs that were contacted with a gold-coated

Atomic Force Microscopy (CP-AFM) tip or with the eutectic alloy of gallium and

indium (EGaIn) showed that the cross-conjugated anthraquinone unit reduced the

conductance by about a factor fifty, compared to the linear conjugated anthracene

unit. A similar reduction of the conductance was found when the conjugation

pattern was broken, by incorporation of a dihydroanthracene unit. This trend was

less clearly displayed in LAMJs. Single molecule experiments by Mechanically

Controllable Break Junction (MCBJ) methods gave about two orders of magnitude

lower conductances for the anthraquinone wire than for the anthracene-based wire,

in good agreement with the other measurements. Transport calculations revealed a

strong minimum in the transmission of the anthraquinone-wire around the Fermi

energy. The reduction of the conductance of the cross-conjugated anthraquinone-

based wire can be attributed to this quantum interference effect.

In Chapter 6 we have incorporated the aromatic methano[10]annulene unit (10 π-

electrons) into molecular wires and thiophene-based polymers and compared it to

naphthalene, to study the influence of aromaticity on the conductance of

molecular wires and on the conductivity of conjugated polymers. We observed a

decrease in the optical HOMO-LUMO gap of the methano[10]annulene based

wire and polymer, compared to the naphthalene analogues. This study is still in an

exploratory state.

In Chapter 7 we return to the Matrix Approach by presenting additional results

from conductance measurements by various methods (in several collaborations) on

the length dependence of molecular conductance and on the comparison of

monothiolated and dithiolated molecular wires. We present an overview of all

conductance measurement results on our series of wires, obtained by different

collaborating groups in different junctions. The results obtained in Au-molecule-

Au junctions (CP-AFM, STM-BJ, and MCBJ) showed an identical dependence of

the conductance on the length of the linear conjugated molecular wires, expressed

in values of 0.33-0.35 Åβ -1. Significant decreases in HOMO-LUMO gap resulted

only in a small deviation from this length dependence. The molecular conductance

was however changed by about two orders of magnitude when the conjugation

pattern was changed into cross-conjugated or broken conjugation. This latter trend

was also found in junctions over larger areas that have a more complex top contact

(e.g., GaIn/Ga2O3 in EGaIn junctions or Au/PEDOT:PSS in LAMJs). In these

213

Summary

junctions the estimated values for the conductance per molecule were lower and

the length dependence was less strong than for Au-molecule-Au junctions, which is

attributed to the less conductive interlayer between the SAM and the metal

electrode. The mentioned dependence of the molecular conductance on the

conjugation pattern, which can be described by quantum interference effects, offers

an interesting tool to control the conductance of single molecules and SAMs as

required for electronic applications. As such, these fundamental studies can

contribute to the development of molecular electronic switching and computing.

214

Samenvatting

SamenvattingDit proefschrift gaat over het geleiden van

elektrische stroom door moleculen. Dat koperdraad

stroom geleidt, weten we al sinds de eerste

elektrische experimenten. We hebben ook geleerd

dat we onszelf tegen deze stroom kunnen

beschermen door de koperdraden in te pakken in een plastic, zoals we zien bij

elektriciteitskabels aan apparatuur en in gebouwen. Dit plastic geleidt geen stroom.

Het is echter mogelijk om met dezelfde atomaire elementen (koolstof en waterstof)

moleculen en plastics te maken die wél stroom kunnen geleiden of zelfs stroom

kunnen opwekken uit zonne-energie (organische zonnecellen). De moleculen in

deze materialen zijn herkenbaar aan de combinatie van dubbele en enkele

bindingen tussen de koolstofatomen die het skelet van het molecuul vormen. Dit

noemen we π-conjugatie.

Voor het bestuderen van elektrische geleiding door moleculen hebben we series

langwerpige π-geconjugeerde moleculen gemaakt: moleculaire stroomdraadjes van

ongeveer twee miljoenste milimeter groot. In deze series variëren we steeds het

middenstuk van het molecuul, terwijl de uiteinden in al onze moleculaire draadjes

dezelfde structuur hebben: verbonden aan het middenstuk zitten acetyleengroepen

(drievoudige bindingen, die het molecuul vrij star maken) met daaraan

fenylgroepen (benzeenringen), met aan de uiteinden een zwavelatoom

(thiolgroepen). We hebben al deze moleculen op dezelfde manier gebouwd uit

onderdelen, waarbij we het (steeds verschillende) middenstuk koppelen met de

acetylenen, waaraan de fenylgroepen

met tert-butylgroepen beschermde

zwavelatomen vast zitten. In een laatste

stap verwisselen we deze

beschermgroepen van de zwavelatomen

door acetylgroepen, die gemakkelijker

van de thiolen af te halen zijn als we

moleculen willen verbinden met

elektrodes. De beschermgroepen zijn

noodzakelijk om te voorkomen dat de

moleculen oxideren aan lucht,

215

Figuur 2 Schema voor de synthese van moleculaire stroomdraadjes. De bindingen tussen de koolstofatomen zijn getekend, maar de atomen zelf niet. Het grijze middenstuk is verschillende voor elk draadje.

Figuur 1 Multimeter.

Samenvatting

waardoor ze met hun twee thiol-eindgroepen aan elkaar zouden komen te zitten en

zo onoplosbare polymeren vormen, waar we niets meer mee kunnen doen.

Voor het verbinden van de moleculen aan de gouden elektrodes maken we gebruik

van de sterke binding die zwavelatomen aangaan met goud. Moleculen met thiol-

eindgroepen kunnen zichzelf vanuit een oplossing op een goudoppervlak naast

elkaar staand organiseren tot lagen van slechts één molecuul dik, die we

monolagen of SAMs noemen. Als er nog acetylbeschermgroepen op de thiolen

zitten, dan vormen zich wel monolagen, maar de moleculen staan niet maximaal

dicht naast elkaar: er blijven gaten over in de SAM. Om deze gaten te kunnen

vullen en zo een dichte SAM te krijgen, moeten we de acetylbeschermgroep van

één van beide thiolen afhalen. Zo vormt zich een negatief geladen zwavelatoom

aan het molecuul dat erg snel met goud reageert en daardoor de laatste gaatjes vult

met dit soort moleculen. We hebben ontdekt dat we dit ontschermen kunnen

bereiken door triethylamine toe te voegen aan de oplossing van de moleculaire

stroomdraadjes en dat het vormen van dichtgepakte SAMs ongeveer twee dagen

duurt. Het is mogelijk om sneller SAMs te maken door gebruik te maken van het

216

Figuur 3 Vorming van SAMs op een goud oppervlak. De moleculaire draadjes worden eerst opgelost in het oplosmiddel THF. Als we daar een goud oppervlak inleggen, vormt zich gedurende twee dagen wel een laagje, maar de moleculen staan niet maximaal dicht naast elkaar (situatie a.). Als we aan deze oplossing van draadjes in THF triethylamine (Et3N) toevoegen, vormen zich in twee dagen tijd wel dichtgepakte SAMs van hoge kwaliteit (situatie b.). Voor het sneller vormen van laagjes, kunnen we tetrabutylammonium hydroxide gebruiken (situatie c.). Als we daarvan echter te veel toevoegen, dan gaan de moleculen plat op het goud liggen (situatie d.).

Samenvatting

reactievere tetrabutylammonium hydroxide. Dit haalt binnen een paar seconden de

acetyl-beschermgroepen van de thiolen, waarna zich in ongeveer één uur tijd een

SAM vormt. Het is echter belangrijk niet te veel tetrabutylammonium hydroxide

toe te voegen, want dan worden de acetylgroepen verwijderd van beide thiolen en

binden deze beide aan het goud, waardoor de moleculen plat gebonden liggen op

het goud. Dit laatste maakt het meten van de geleiding tussen beide uiteinden van

het molecuul onmogelijk.

Nadat we de moleculaire stroomdraadjes hadden gemaakt en onderzocht hadden

hoe deze verbonden konden worden aan de goudelektrodes, konden we de

geleiding van de moleculen gaan bestuderen. Hiervoor hebben we samengewerkt

met verschillende groepen die daar experts in zijn, maar allemaal met verschillende

technieken deze geleidingsmetingen doen. Het is namelijk mogelijk om

geleidingsmetingen te doen aan één enkel molecuul, maar ook aan honderden of

miljarden moleculen tegelijk en daarvan toch iets te leren over de geleiding per

molecuul.

Voor het meten van de geleiding door miljarden moleculen tegelijk wordt eerst een

SAM gevormd op een goudoppervlak (de ene elektrode). Het is hierbij cruciaal dat

de moleculen in de SAM allemaal netjes rechtop staan en er geen gaten in de laag

zitten. Vervolgens moet de tweede elektrode worden aangebracht op de bovenkant

van de SAM. Daarvoor is een zacht materiaal nodig om te voorkomen dat de

bovenste elektrode door de SAM heengaat en zo rechtstreeks contact maakt met de

bodemelektrode. Een mogelijk materiaal is het geleidende polymeer PEDOT:PSS,

217

Figuur 4 Methoden voor de meting van geleiding door vele moleculen parallel. Eerst wordt een SAM gevormd op een goud oppervlak (de bodemelektrode). Daarna wordt de topelektrode op de SAM aangebracht. In LAMJ is deze topelektrode het polymeer PEDOT:PSS, met daarop nog een extra laagje goud om het meten handiger te maken. De topelektrode in EGaIn juncties bestaat uit de vloeibare legering van gallium en indium, met een dun laagje galliumoxide. In CP-AFM juncties is de (van een laagje goud voorziene) tip van de atoomkrachtmicroscoop het de bovenste elektrode.

Samenvatting

dat als suspensie in water wordt aangebracht. Nadat het water is verdampt blijft

een laagje polymeer over waarop goud kan worden aangebracht. Dit wordt

gebruikt in de techniek die we afkorten als LAMJ. Een alternatief materiaal is de

(bij kamertemperatuur vloeibare) legering van gallium en indium, EGaIn. De

topelektrode kan ook gevormd worden door de tip van een

atoomkrachtmicroscoop (CP-AFM). Zo'n tip kan vergeleken worden met de naald

van een platenspeler. Het is belangrijk dat deze tip van een laagje goud is voorzien

en dat hij maar heel losjes op de SAM duwt. Op deze manier kan de stroom door

een paar honderd naast elkaar staande moleculen worden gemeten.

De geleiding van een enkel molecuul kan worden gemeten door een heel klein

contact tussen de twee goudelektrodes te maken, in aanwezigheid van de

moleculaire stroomdraadjes (die her en der met hun thiol-eindgroepen aan het

goud vastzitten). De twee elektrodes worden vervolgens uit elkaar getrokken,

waarbij het aantal goudatomen dat de twee verbindt afneemt, totdat ook het laatste

atoom in de breekjunctie loslaat. Dan is er een kans dat het molecuul dat in de

buurt zat van dit laatste atoom nog aan beide elektrodes vastzit. Zo kan de

geleiding door dit molecuul worden gemeten. Bij het verder uit elkaar trekken van

de elektrodes van de breekjunctie laat het molecuul op een gegeven moment los en

verdwijnt de geleiding. Doordat we hier te maken hebben met een kans om de

geleiding van een enkel molecuul te meten is het belangrijk deze meting honderden

of duizend keren te herhalen. Als een bepaalde geleidingswaarde dan heel vaak

gemeten wordt, wordt deze beschouwd als de meest waarschijnlijke waarde voor

de geleiding van een molecuul.

218

Figuur 5 Door de breekjunctie steeds verder te openen in aanwezigheid van moleculaire stroomdraadjes, is er een kans op de vorming van een goud-molecuul-goud contact. Op dat moment kan de geleiding van het molecuul worden gemeten.

Samenvatting

Het meten van de geleiding van series π-geconjugeerde moleculaire stroomdraadjes

heeft ons geleerd dat de geleiding exponentieel afneemt als het draadje langer

wordt. Dit effect is het sterkste bij metingen aan een enkel molecuul en metingen

met CP-AFM, waarbij in beide gevallen de moleculen direct verbonden zijn aan

twee goudelektrodes. De metingen met LAMJ gaven dezelfde trend, maar dan

minder sterk. Ondergeschikt aan de lengteafhankelijkheid is het energieniveau van

de hoogste met elektronen gevulde moleculaire orbitaal (HOMO). Hoe hoger de

HOMO ligt in energie, hoe groter de moleculaire geleiding.

Een andere strategie om moleculaire geleiding te beïnvloeden berust op de π-

conjugatie van de moleculen. De moleculaire geleiding is een stuk lager als we het

patroon van enkele en dubbele bindingen tussen de koolstofatomen (lineaire

conjugatie) verbreken. Dat kan door koolstofatomen zonder dubbele bindingen te

gebruiken (verbroken conjugatie), of door middel van kruisconjugatie. In dit laatste

geval maken we een driesprong en zijn beide kanten van het molecuul linear

geconjugeerd met de zijweg maar niet met elkaar. In de praktijk bereiken we dit

door een anthrachinongroep in te bouwen in onze moleculaire stroomdraadjes. In

deze anthrachinongroep vormen de dubbelgebonden zuurstofatomen de zijweg die

het molecuul kruisgeconjugeerd maken. De lage geleiding door dit

kruisgeconjugeerde moleculaire draadje wordt waarschijnlijk veroorzaakt door een

effect dat we kwantuminterferentie noemen. De elektronen die door het draadje

gaan kunnen we beschouwen als deeltjes, maar ook als golven. Een manier om

naar deze kwantuminterferentie te kijken is als volgt: een deel van deze golven

neemt de zijweg (naar het zuurstofatoom), maar komt erachter dat deze doodloopt

219

Figuur 6 Twee series moleculaire stroomdraadjes. De geleidingswaarden zijn gemeten in goud-molecuul-goud juncties.

Samenvatting

en moet rechtsomkeert maken. Hierbij komen ze echter weer heengaande golven

tegen en deze doven elkaar uit. Hierdoor loopt er netto maar heel weinig stroom

van de ene elektrode naar de andere.

De kruisgeconjugeerde anthrachinongroep zorgt dus voor een lage geleiding. Het

mooie van de anthrachinongroep is echter dat we deze kunnen schakelen. Het

moleculaire anthrachinondraadje kan in een oplossing worden gereduceerd met

behulp van elektrochemie of door toevoeging van een chemische reductor. Daarbij

worden twee elektronen toegevoegd aan het molecuul, waardoor de

kruisgeconjugeerde anthrachinongroep verandert in een lineair geconjugeerde

220

Figuur 7 Kwantuminterferentie in de elektrische geleiding van kruisgeconjugeerde moleculen is te vergelijken met het schaatsen van de elfstedentocht. Bij Bartlehiem moeten alle schaatsers linksaf slaan om in Dokkum de tiende stempel te halen. Vanuit Dokkum schaatsen ze hetzelfde stuk weer terug richting Bartlehiem. Nu weten schaatsers dat ze opnieuw bij Bartlehiem aangekomen, door moeten schaatsen richting de finish in Leeuwarden, in plaats van terug richting Franeker. Bovendien zullen ze hun uiterste best doen om niet tegen elkaar op te botsen. Elektronen die echter net zo'n route moeten volgen door het molecuul (een zijweg in en vervolgens dat stukje weer terug), zijn minder intelligent. Ze kunnen op het stukje tweerichtingsverkeer naar Dokkum tegen elkaar aanbotsen en als ze al vanuit Dokkum terugkomen bij Bartlehiem, dan is het nog maar de vraag of ze weten dat ze dan naar Leeuwarden moeten in plaats van naar Franeker. Al met al zal het een flinke chaos worden met veel valpartijen en zullen slechts weinig elektronen de finish in Leeuwarden weten te bereiken.

Samenvatting

anthraceengroep. Deze groep kan vervolgens weer terug worden geschakeld naar

de originele anthrachinongroep door oxidatie. We verwachten zo snel te kunnen

schakelen tussen een lage en een hoge geleiding door middel van het toevoegen en

verwijderen van elektronen. Deze lage en hoge geleiding, kun je beschouwen als

respectievelijk een "0" en een "1" en daarmee dus als een bit in een computer. Dit

principe zouden we echter kunnen gebruiken om een stap verder te gaan en

complete elektronische schakelingen in elektronica te vervangen door π-

geconjugeerde moleculen. In dit proefschrift hebben we daarvoor de basisprincipes

onderzocht en we hebben een moleculaire elektronische schakelaar ontwikkeld.

221

Figuur 8 Een moleculaire elektronische schakelaar, gebonden aan goudelektrodes.

Samenvatting

222

Dankwoord

Dankwoord (Acknowledgements)Na veel synthetiseren, meten, analyseren, praten, denken en typen zit mijn

promotieonderzoek erop. Hier ligt het resultaat. Dat zou niet gelukt zijn zonder de

hulp en steun van heel veel mensen, die ik hier graag wil bedanken.

In de eerste plaats noem ik Kees. Bedankt voor de jaren dat ik in jouw groep heb

mogen werken en dat je mij als wetenschapper hebt willen opvoeden. Bedankt ook

voor alle vrijheid die je mij hebt gegeven. Soms vond ik dat lastig, maar ik heb

vooral heel veel kunnen leren. Ik mocht de richting van mijn onderzoek bepalen en

samenwerkingspartners zoeken, maar kon ook altijd bij jou terecht voor advies of

om te verifiëren of jij achter deze keuzes stond. Marcel, Thomas, and Herre, a

word of gratitude for your careful reading and approving of my manuscript.

Sense Jan, jouw betrokkenheid bij dit project vond al heel wat jaren geleden haar

oorsprong. Fijn dat je, eenmaal gevestigd in Leiden, ook weer met ons wilde

samenwerken. En tof dat jij en Constant afgelopen voorjaar de handschoen

oppakten om te gaan CP-AFM'men aan mijn SAMs. Constant, ik heb genoten van

onze tijd in Leiden en veel van jou geleerd tijdens de dagen achter de AFM. En

gaaf dat jouw grondige data-analyse zulke mooie resultaten heeft opgeleverd. Eek,

met jou heb ik ook lange tijd mogen samenwerken. Je beschikte over veel geduld

toen je mij de basis van de natuurkunde achter de moleculaire elektronica

bijbracht. Bert en jij hebben mij overtuigd van het belang van systematische series

voor de moleculaire elektronica. Deze zijn de basis geworden van dit proefschrift.

Het is jammer dat mijn moleculen niet in Groninger breekjuncties zijn beland,

maar door jouw overstap naar de LAMJs heb je mij ook met die techniek in

aanraking gebracht. Ook mochten we samen beginnen aan de puzzel van het

maken van goede SAMs.

Dago, Paul, Tom, Ilias en Auke, ik waardeer het dat jullie de wafers met LAMJs

voor en met mij hebben gemaakt, gemeten, geanalyseerd en geïnterpreteerd. En

natuurlijk dank voor alle discussies en antwoorden. Christian, Roel, Herre en Jan:

door jullie onmisbare interesse in mijn moleculen en procedures zijn mijn draadjes

toch in breekjuncties terecht gekomen. Diana en Mickael, tof dat jullie het stokje

hebben willen overnemen. Ik ben benieuwd wat er nog komen gaat...! Ook heb ik

de leerzame discussies met jullie erg gewaardeerd, bedankt, ook aan Ferry en Jos.

Thomas, Bhadra, Wenjing, and Pavel, thanks for studying my molecules in your

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Acknowledgements

STM-BJ and MCBJ setups and for all beautiful results. Davide and Ryan, our

collaboration on the EGaIn junctions started only a year ago, but yielded nice

results. Ryan, a word of thanks for your help with the writing of our SAMs article.

Victor and Colin, your transport calculations in Chapter 4 and those of Troels and

Kristian in Chapter 5 really supported the experimental results. Kim, your

invitation to Twente and help with the electrochemical experiments meant a lot to

me. Alex, you learned me how to use Zotero and gave me access to titan. This

helped me a great deal, especially during the writing of my thesis.

Marleen, jij hebt mij aanvankelijk geënthousiasmeerd voor dit onderzoek. Samen

met Daniel heb je mij begeleid tijdens mijn afstudeerproject, waarvan de resultaten

een onderdeel van hoofdstuk 2 vormen. Daniel, I want to thank you for your help

and guidance. Petra, Jelmer en Jurjen, jullie waren de eerste studenten die ik mocht

begeleiden. Jullie hebben geholpen bij de opbouw van de bibliotheek van

moleculaire stroomdraadjes. Bedankt voor al het synthetische werk dat jullie

hebben verzet! Rene, Jorrit, Jeroen, Erik en Alexander, jullie zullen bekende

structuren terugvinden in hoofdstuk 6. Ook jullie bedankt voor jullie synthetische

bijdragen. Jochem, dankzij jou heb ik van alles geleerd over FETs en bedankt voor

je Mathematicawerk. Reinder, je technische ondersteuning van dit onderzoek

maakte voor mij een groot verschil. Renate, ik heb genoten van jouw hulp en

gezelligheid! Groepsleden Alfred, Cindy, Davide, Jelmer, Jeremio, Mehrnoosh,

Parisa, Ricardo, Thomas, Wenjing, bedankt voor alles. Oud-groepsleden Alex,

Carlos, Floris, Frank, Hang, Lacra, Patrick, Renske, Xiaonan, ook jullie bedankt.

Alex, Minze en Renske, gaaf om met elkaar samen te schaatsen en te skaten op de

dinsdag; dat was een welkome en noodzakelijke afleiding. Anne en Cindy, ik heb

genoten van jullie gezelligheid in San Francisco en op andere trips. MEPOS’sers,

bedankt voor de gezelligheid bij uitjes en activiteiten en voor het gebruik van jullie

apparatuur. Petra Rudolf, Titiana, Régis, Olekssi en Hans, bedankt voor toegang

tot en hulp bij XPS en UPS. Nathalie en Johan, jullie STM-adviezen heb ik op prijs

gesteld, ook al ben ik later een andere kant op gegaan met mijn onderzoek. Harry

Jonkman, bedankt ook voor jouw adviezen en uitleg. Ook wil ik graag Theodora

bedanken voor de massa's, Pieter voor alle hulp met NMR'ren, Wim Huibers en

Frank voor de GPC, Jia en Jochem voor fluorescentielevensduurmetingen, Wesley

voor spectroelectrochemie en Ben Hesp voor hulp bij spectroscopische problemen.

Ben Bosman, Stijntje en de anderen van het magazijn, fijn dat jullie altijd voor ons

klaarstaan. Ook bedankt aan de schoonmakers en alle anderen die ons werk

mogelijk maken. Rink, bedankt voor je adviezen en het begeleiden van de

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Dankwoord

donderdagse sporturen. Daarmee heb je me door de schrijffase heen geholpen.

Bart en Roelie, jullie hebben de omslag van dit proefschrift ontworpen met veel

enthousiasme. Ik vond het prettig dat ik me daarover geen zorgen hoefde te maken.

Jorien en Parisa, het is voor mij een eer jullie als paranimfen te hebben. Jorien en

Harm Jan, Tjard en Margreet, Jaco en Jacolien, Karin en Peter, Ilona, en Els,

bedankt voor jullie vriendschap! Lieve ouders en schoonouders, bedankt dat jullie

altijd voor ons klaarstaan. Ook bedankt aan mijn broers/zwagers/schoonzussen

Jelte en Catharina, Jos, Gerrit en Jorine, Martien, Bart en Roelie, Stephan, en

Daniëlle voor de warme families die we vormen. Opa en oma de Groot en oma

Roos, ook jullie bedankt.

Jeroen, ik kan niet in woorden uitdrukken wat jij als man en maatje voor mij

betekent. Ik waardeer de talloze keren dat er een heerlijke maaltijd voor me

klaarstond na een lange dag werk en je geduld tijdens de vele uren die ik achter de

computer heb doorgebracht. Ik zie uit naar ons nieuwe avontuur samen! Tot slot

ben ik dank verschuldigd aan mijn God en Vader, oorsprong en bestemming, voor

Zijn onbeschrijflijke liefde en trouw, maar ook voor de talenten en kracht om dit

promotieonderzoek uit te voeren.

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